chr6-14173197-G-A

Variant names:

• chr6-14173197-G-A
• rs853356
• ENST00000650535.1:n.107-18487C>T

Variant summary

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

The ENST00000650535.1(ENSG00000285639):​n.107-18487C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.26 in 151,954 control chromosomes in the GnomAD database, including 5,799 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 0.26 (5799 hom., cov: 32)
• Consequence: ENSG00000285639 ENST00000650535.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.451
• Publications: 7 publications found

Genes affected

ENSG00000285639 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.604 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285639	ENST00000650535.1	n.107-18487C>T		intron_variant	Intron 1 of 1
ENSG00000285639	ENST00000724695.1	n.120-7017C>T		intron_variant	Intron 1 of 3
ENSG00000285639	ENST00000724696.1	n.120-7023C>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.260 AC: 39453 AN: 151836 Hom.: 5786 Cov.: 32

Gnomad AFR AF: 0.292

Gnomad AMI AF: 0.338

Gnomad AMR AF: 0.240

Gnomad ASJ AF: 0.180

Gnomad EAS AF: 0.622

Gnomad SAS AF: 0.454

Gnomad FIN AF: 0.219

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.213

Gnomad OTH AF: 0.262

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

GnomAD4 genome AF: 0.260 AC: 39501 AN: 151954 Hom.: 5799 Cov.: 32 AF XY: 0.264 AC XY: 19636 AN XY: 74260

African (AFR) AF: 0.292 AC: 12105 AN: 41416

American (AMR) AF: 0.240 AC: 3664 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.180 AC: 626 AN: 3472

East Asian (EAS) AF: 0.622 AC: 3207 AN: 5154

South Asian (SAS) AF: 0.452 AC: 2171 AN: 4800

European-Finnish (FIN) AF: 0.219 AC: 2309 AN: 10544

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.213 AC: 14464 AN: 67970

Other (OTH) AF: 0.269 AC: 568 AN: 2112

Alfa AF: 0.241 Hom.: 6600

Bravo AF: 0.262

Asia WGS AF: 0.535 AC: 1857 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.4
DANN	Benign	0.48
PhyloP100		0.45

Splicing

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

Other links and lift over

dbSNP: rs853356; hg19: chr6-14173428;