6-31158201-A-T

Variant names:

• chr6-31158201-A-T
• rs3130455
• ENST00000376266.9:c.-86T>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000376266.9(CCHCR1):​c.-86T>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.179 in 146,138 control chromosomes in the GnomAD database, including 2,444 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.18 (2411 hom., cov: 30)
  • Exomes 𝑓: 0.17 (33 hom.)
• Consequence: CCHCR1 ENST00000376266.9 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.646
• Publications: 14 publications found

Genes affected

CCHCR1 (HGNC:13930): (coiled-coil alpha-helical rod protein 1) This gene encodes a protein with five coiled-coil alpha-helical rod domains that is thought to act as a regulator of mRNA metabolism through its interaction with mRNA-decapping protein 4. It localizes to P-bodies, the site of mRNA metabolism, with an N-terminus that is required for this subcellular localization, suggesting it is a P-body component. Naturally occurring mutations in this gene are associated with psoriasis. [provided by RefSeq, May 2017]

TCF19 (HGNC:11629): (transcription factor 19) This gene encodes a protein that contains a PHD-type zinc finger domain and likely functions as a transcription factor. The encoded protein plays a role proliferation and apoptosis of pancreatic beta cells. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2016]

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.42).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.221 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000376266.9. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCHCR1	NM_001394642.1		c.-202T>A		upstream_gene	N/A	NP_001381571.1	Q8TD31-1
	CCHCR1	NM_001394643.1		c.-229T>A		upstream_gene	N/A	NP_001381572.1	Q8TD31-1
	CCHCR1	NM_001394644.1		c.-152T>A		upstream_gene	N/A	NP_001381573.1	Q8TD31-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCHCR1	ENST00000376266.9	TSL:1	c.-86T>A		5_prime_UTR	Exon 1 of 18	ENSP00000365442.5	Q8TD31-1
	CCHCR1	ENST00000396263.6	TSL:5	c.-152T>A		5_prime_UTR	Exon 1 of 16	ENSP00000379561.2	A2ABH1
	CCHCR1	ENST00000448141.6	TSL:3	c.-82T>A		5_prime_UTR	Exon 1 of 5	ENSP00000414323.2	E7EPK4

Frequencies

GnomAD3 genomes AF: 0.179 AC: 25820 AN: 144384 Hom.: 2407 Cov.: 30

Gnomad AFR AF: 0.152

Gnomad AMI AF: 0.346

Gnomad AMR AF: 0.112

Gnomad ASJ AF: 0.179

Gnomad EAS AF: 0.0422

Gnomad SAS AF: 0.132

Gnomad FIN AF: 0.150

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.224

Gnomad OTH AF: 0.162

GnomAD4 exome AF: 0.167 AC: 277 AN: 1660 Hom.: 33 Cov.: 0 AF XY: 0.149 AC XY: 141 AN XY: 948

African (AFR) AF: 0.100 AC: 1 AN: 10

American (AMR) AF: 0.0522 AC: 12 AN: 230

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 6

East Asian (EAS) AF: 0.00 AC: 0 AN: 18

South Asian (SAS) AF: 0.150 AC: 38 AN: 254

European-Finnish (FIN) AF: 0.250 AC: 3 AN: 12

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2

European-Non Finnish (NFE) AF: 0.199 AC: 214 AN: 1078

Other (OTH) AF: 0.180 AC: 9 AN: 50

GnomAD4 genome AF: 0.179 AC: 25829 AN: 144478 Hom.: 2411 Cov.: 30 AF XY: 0.174 AC XY: 12204 AN XY: 70048

African (AFR) AF: 0.152 AC: 5846 AN: 38440

American (AMR) AF: 0.112 AC: 1617 AN: 14442

Ashkenazi Jewish (ASJ) AF: 0.179 AC: 607 AN: 3394

East Asian (EAS) AF: 0.0423 AC: 207 AN: 4888

South Asian (SAS) AF: 0.131 AC: 586 AN: 4472

European-Finnish (FIN) AF: 0.150 AC: 1414 AN: 9416

Middle Eastern (MID) AF: 0.233 AC: 67 AN: 288

European-Non Finnish (NFE) AF: 0.224 AC: 14856 AN: 66234

Other (OTH) AF: 0.159 AC: 320 AN: 2010

Alfa AF: 0.188 Hom.: 410

Bravo AF: 0.168

Asia WGS AF: 0.0750 AC: 263 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.42
CADD	Benign	12
DANN	Benign	0.78
PhyloP100		0.65
PromoterAI		0.069	Neutral
Mutation Taster		=300/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs3130455; hg19: chr6-31125978;