6-31216419-A-G

Variant names:

• chr6-31216419-A-G
• rs3869109

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 0.589 in 152,042 control chromosomes in the GnomAD database, including 26,562 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 0.59 (26562 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.888
• Publications: 76 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.612 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: 0.589 AC: 89526 AN: 151924 Hom.: 26533 Cov.: 32

Gnomad AFR AF: 0.608

Gnomad AMI AF: 0.486

Gnomad AMR AF: 0.622

Gnomad ASJ AF: 0.659

Gnomad EAS AF: 0.443

Gnomad SAS AF: 0.530

Gnomad FIN AF: 0.668

Gnomad MID AF: 0.633

Gnomad NFE AF: 0.571

Gnomad OTH AF: 0.614

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

GnomAD4 genome AF: 0.589 AC: 89601 AN: 152042 Hom.: 26562 Cov.: 32 AF XY: 0.594 AC XY: 44178 AN XY: 74330

African (AFR) AF: 0.608 AC: 25199 AN: 41458

American (AMR) AF: 0.622 AC: 9498 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.659 AC: 2286 AN: 3470

East Asian (EAS) AF: 0.444 AC: 2300 AN: 5180

South Asian (SAS) AF: 0.530 AC: 2554 AN: 4820

European-Finnish (FIN) AF: 0.668 AC: 7061 AN: 10578

Middle Eastern (MID) AF: 0.633 AC: 186 AN: 294

European-Non Finnish (NFE) AF: 0.571 AC: 38782 AN: 67956

Other (OTH) AF: 0.613 AC: 1293 AN: 2110

Alfa AF: 0.579 Hom.: 65870

Bravo AF: 0.590

Asia WGS AF: 0.566 AC: 1969 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	3.4
DANN	Benign	0.18
PhyloP100		-0.89

Splicing

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

Other links and lift over

dbSNP: rs3869109; hg19: chr6-31184196;