6-135110180-T-C

Variant names:

• chr6-135110180-T-C
• rs6920211
• ENST00000844074.1:n.272+44T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000844074.1(ENSG00000309813):​n.272+44T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.285 in 152,000 control chromosomes in the GnomAD database, including 6,721 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 0.29 (6721 hom., cov: 32)
• Consequence: ENSG00000309813 ENST00000844074.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.477
• Publications: 12 publications found

Genes affected

ENSG00000309813 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.382 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000844074.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000309813	ENST00000844074.1		n.272+44T>C		intron	N/A
	ENSG00000309813	ENST00000844075.1		n.253+36T>C		intron	N/A
	ENSG00000309813	ENST00000844076.1		n.248+41T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.285 AC: 43309 AN: 151882 Hom.: 6699 Cov.: 32

Gnomad AFR AF: 0.387

Gnomad AMI AF: 0.116

Gnomad AMR AF: 0.236

Gnomad ASJ AF: 0.220

Gnomad EAS AF: 0.273

Gnomad SAS AF: 0.106

Gnomad FIN AF: 0.327

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.248

Gnomad OTH AF: 0.250

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.285 AC: 43369 AN: 152000 Hom.: 6721 Cov.: 32 AF XY: 0.282 AC XY: 20975 AN XY: 74288

African (AFR) AF: 0.387 AC: 16051 AN: 41426

American (AMR) AF: 0.236 AC: 3609 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.220 AC: 764 AN: 3470

East Asian (EAS) AF: 0.273 AC: 1412 AN: 5164

South Asian (SAS) AF: 0.106 AC: 512 AN: 4822

European-Finnish (FIN) AF: 0.327 AC: 3446 AN: 10542

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.248 AC: 16867 AN: 67978

Other (OTH) AF: 0.252 AC: 531 AN: 2108

Alfa AF: 0.261 Hom.: 19576

Bravo AF: 0.289

Asia WGS AF: 0.203 AC: 705 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.4
DANN	Benign	0.26
PhyloP100		-0.48

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6920211;

hg19: chr6-135431318;

COSMIC: COSV60283445;