6-164179816-C-T

Variant names:

• chr6-164179816-C-T
• rs1894638
• ENST00000850151.1:n.312-57938C>T

Variant summary

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

The ENST00000850151.1(ENSG00000288696):​n.312-57938C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.395 in 152,002 control chromosomes in the GnomAD database, including 13,753 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 0.40 (13753 hom., cov: 32)
• Consequence: ENSG00000288696 ENST00000850151.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.385
• Publications: 4 publications found

Genes affected

ENSG00000288696 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.48 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
ENSG00000288696	ENST00000850151.1	n.312-57938C>T		intron_variant	Intron 3 of 4
ENSG00000288696	ENST00000850152.1	n.372-57938C>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.396 AC: 60081 AN: 151884 Hom.: 13751 Cov.: 32

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.439

Gnomad AMR AF: 0.489

Gnomad ASJ AF: 0.604

Gnomad EAS AF: 0.415

Gnomad SAS AF: 0.382

Gnomad FIN AF: 0.559

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.482

Gnomad OTH AF: 0.453

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

GnomAD4 genome AF: 0.395 AC: 60089 AN: 152002 Hom.: 13753 Cov.: 32 AF XY: 0.403 AC XY: 29913 AN XY: 74294

African (AFR) AF: 0.154 AC: 6384 AN: 41492

American (AMR) AF: 0.489 AC: 7465 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.604 AC: 2092 AN: 3466

East Asian (EAS) AF: 0.414 AC: 2131 AN: 5146

South Asian (SAS) AF: 0.385 AC: 1850 AN: 4804

European-Finnish (FIN) AF: 0.559 AC: 5909 AN: 10564

Middle Eastern (MID) AF: 0.582 AC: 171 AN: 294

European-Non Finnish (NFE) AF: 0.482 AC: 32733 AN: 67950

Other (OTH) AF: 0.454 AC: 956 AN: 2108

Alfa AF: 0.300 Hom.: 1348

Bravo AF: 0.382

Asia WGS AF: 0.341 AC: 1187 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.56
DANN	Benign	0.62
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs1894638; hg19: chr6-164600848;