rs1634747

Variant names:

• chr6-31314099-G-A
• rs1634747

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 0.407 in 144,886 control chromosomes in the GnomAD database, including 16,116 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 0.41 (16116 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.249

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.413 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: 0.407 AC: 58949 AN: 144772 Hom.: 16108 Cov.: 28

Gnomad AFR AF: 0.400

Gnomad AMI AF: 0.538

Gnomad AMR AF: 0.343

Gnomad ASJ AF: 0.402

Gnomad EAS AF: 0.283

Gnomad SAS AF: 0.396

Gnomad FIN AF: 0.522

Gnomad MID AF: 0.432

Gnomad NFE AF: 0.417

Gnomad OTH AF: 0.374

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

GnomAD4 genome AF: 0.407 AC: 58993 AN: 144886 Hom.: 16116 Cov.: 28 AF XY: 0.408 AC XY: 28741 AN XY: 70474

Gnomad4 AFR AF: 0.400

Gnomad4 AMR AF: 0.344

Gnomad4 ASJ AF: 0.402

Gnomad4 EAS AF: 0.284

Gnomad4 SAS AF: 0.396

Gnomad4 FIN AF: 0.522

Gnomad4 NFE AF: 0.417

Gnomad4 OTH AF: 0.370

Alfa AF: 0.412 Hom.: 4190

Asia WGS AF: 0.323 AC: 1089 AN: 3370

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.4
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1634747; hg19: chr6-31281876;