6-31583760-C-G

Variant names:

• chr6-31583760-C-G
• rs3093562

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 0.0765 in 152,008 control chromosomes in the GnomAD database, including 597 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 0.076 (597 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.519
• Publications: 8 publications found

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 (NFE) allele frequency at 95% confidence interval = 0.111 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: 0.0766 AC: 11630 AN: 151892 Hom.: 599 Cov.: 31

Gnomad AFR AF: 0.0207

Gnomad AMI AF: 0.106

Gnomad AMR AF: 0.0636

Gnomad ASJ AF: 0.129

Gnomad EAS AF: 0.00559

Gnomad SAS AF: 0.0319

Gnomad FIN AF: 0.117

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.113

Gnomad OTH AF: 0.0687

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

GnomAD4 genome AF: 0.0765 AC: 11627 AN: 152008 Hom.: 597 Cov.: 31 AF XY: 0.0755 AC XY: 5606 AN XY: 74298

African (AFR) AF: 0.0206 AC: 854 AN: 41450

American (AMR) AF: 0.0635 AC: 970 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.129 AC: 447 AN: 3466

East Asian (EAS) AF: 0.00560 AC: 29 AN: 5178

South Asian (SAS) AF: 0.0323 AC: 156 AN: 4824

European-Finnish (FIN) AF: 0.117 AC: 1237 AN: 10532

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.113 AC: 7657 AN: 67984

Other (OTH) AF: 0.0684 AC: 144 AN: 2104

Alfa AF: 0.0454 Hom.: 36

Bravo AF: 0.0715

Asia WGS AF: 0.0270 AC: 98 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	2.4
DANN	Benign	0.43
PhyloP100		0.52

Splicing

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

Other links and lift over

dbSNP: rs3093562; hg19: chr6-31551537;