rs6102185

Variant names:

• chr20-40849893-G-A
• rs6102185
• ENST00000758964.1:n.86+16208C>T

Your query was ambiguous. Multiple possible variants found:

• chr20-40849893-G-A
• chr20-40849893-G-T

Variant summary

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

The ENST00000758964.1(ENSG00000229771):​n.86+16208C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.673 in 151,476 control chromosomes in the GnomAD database, including 34,810 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 0.67 (34810 hom., cov: 29)
• Consequence: ENSG00000229771 ENST00000758964.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.381
• Publications: 5 publications found

Genes affected

ENSG00000229771 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.775 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
ENSG00000229771	ENST00000758964.1	n.86+16208C>T		intron_variant	Intron 1 of 5

Frequencies

GnomAD3 genomes AF: 0.673 AC: 101935 AN: 151358 Hom.: 34780 Cov.: 29

Gnomad AFR AF: 0.782

Gnomad AMI AF: 0.492

Gnomad AMR AF: 0.583

Gnomad ASJ AF: 0.741

Gnomad EAS AF: 0.606

Gnomad SAS AF: 0.656

Gnomad FIN AF: 0.659

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.636

Gnomad OTH AF: 0.664

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

GnomAD4 genome AF: 0.673 AC: 102007 AN: 151476 Hom.: 34810 Cov.: 29 AF XY: 0.668 AC XY: 49408 AN XY: 73912

African (AFR) AF: 0.782 AC: 32291 AN: 41284

American (AMR) AF: 0.582 AC: 8833 AN: 15178

Ashkenazi Jewish (ASJ) AF: 0.741 AC: 2571 AN: 3468

East Asian (EAS) AF: 0.605 AC: 3124 AN: 5160

South Asian (SAS) AF: 0.656 AC: 3110 AN: 4744

European-Finnish (FIN) AF: 0.659 AC: 6887 AN: 10448

Middle Eastern (MID) AF: 0.636 AC: 187 AN: 294

European-Non Finnish (NFE) AF: 0.636 AC: 43166 AN: 67892

Other (OTH) AF: 0.663 AC: 1390 AN: 2098

Alfa AF: 0.647 Hom.: 88427

Bravo AF: 0.672

Asia WGS AF: 0.609 AC: 2118 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.94
DANN	Benign	0.70
PhyloP100		-0.38

Splicing

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

Other links and lift over

dbSNP: rs6102185; hg19: chr20-39478533;