6-31216419-A-G

Variant names:

• chr6-31216419-A-G
• rs3869109

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.608

Gnomad4 AMR AF: 0.622

Gnomad4 ASJ AF: 0.659

Gnomad4 EAS AF: 0.444

Gnomad4 SAS AF: 0.530

Gnomad4 FIN AF: 0.668

Gnomad4 NFE AF: 0.571

Gnomad4 OTH AF: 0.613

Alfa AF: 0.574 Hom.: 37935

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3869109; hg19: chr6-31184196;