rs1634789

Variant names:

• chr6-31309310-G-A
• rs1634789

Your query was ambiguous. Multiple possible variants found:

• chr6-31309310-G-A
• chr6-31309310-G-T

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 0.667 in 147,578 control chromosomes in the GnomAD database, including 36,356 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 (36356 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.81

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.782 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: 0.667 AC: 98403 AN: 147470 Hom.: 36309 Cov.: 30

Gnomad AFR AF: 0.764

Gnomad AMI AF: 0.715

Gnomad AMR AF: 0.793

Gnomad ASJ AF: 0.889

Gnomad EAS AF: 0.688

Gnomad SAS AF: 0.718

Gnomad FIN AF: 0.578

Gnomad MID AF: 0.860

Gnomad NFE AF: 0.575

Gnomad OTH AF: 0.765

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

GnomAD4 genome AF: 0.667 AC: 98503 AN: 147578 Hom.: 36356 Cov.: 30 AF XY: 0.673 AC XY: 48333 AN XY: 71832

Gnomad4 AFR AF: 0.764

Gnomad4 AMR AF: 0.794

Gnomad4 ASJ AF: 0.889

Gnomad4 EAS AF: 0.689

Gnomad4 SAS AF: 0.717

Gnomad4 FIN AF: 0.578

Gnomad4 NFE AF: 0.575

Gnomad4 OTH AF: 0.767

Alfa AF: 0.630 Hom.: 6263

Asia WGS AF: 0.719 AC: 2330 AN: 3240

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.6
DANN	Benign	0.14

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1634789; hg19: chr6-31277087;