rs1634747

chr6-31314099-G-A

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;