6-32931519-C-T

Variant names:

• chr6-32931519-C-T
• rs154978

Variant summary

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

The variant allele was found at a frequency of 0.538 in 152,096 control chromosomes in the GnomAD database, including 22,288 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 0.54 (22288 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.20
• Publications: 36 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.577 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

Frequencies

GnomAD3 genomes AF: 0.538 AC: 81691 AN: 151978 Hom.: 22259 Cov.: 32

Gnomad AFR AF: 0.583

Gnomad AMI AF: 0.458

Gnomad AMR AF: 0.479

Gnomad ASJ AF: 0.393

Gnomad EAS AF: 0.565

Gnomad SAS AF: 0.529

Gnomad FIN AF: 0.557

Gnomad MID AF: 0.609

Gnomad NFE AF: 0.527

Gnomad OTH AF: 0.519

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

GnomAD4 genome AF: 0.538 AC: 81770 AN: 152096 Hom.: 22288 Cov.: 32 AF XY: 0.537 AC XY: 39931 AN XY: 74342

African (AFR) AF: 0.584 AC: 24193 AN: 41460

American (AMR) AF: 0.479 AC: 7326 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.393 AC: 1363 AN: 3472

East Asian (EAS) AF: 0.566 AC: 2928 AN: 5174

South Asian (SAS) AF: 0.528 AC: 2548 AN: 4824

European-Finnish (FIN) AF: 0.557 AC: 5891 AN: 10572

Middle Eastern (MID) AF: 0.603 AC: 175 AN: 290

European-Non Finnish (NFE) AF: 0.527 AC: 35836 AN: 67988

Other (OTH) AF: 0.518 AC: 1094 AN: 2112

Alfa AF: 0.532 Hom.: 76870

Bravo AF: 0.533

Asia WGS AF: 0.560 AC: 1948 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.1
DANN	Benign	0.66
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs154978; hg19: chr6-32899296;