rs1634718

Variant names:

• chr6-31005088-A-G
• rs1634718

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 0.2 in 152,176 control chromosomes in the GnomAD database, including 3,576 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 0.20 (3576 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.420

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.265 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: 0.201 AC: 30489 AN: 152058 Hom.: 3578 Cov.: 32

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.280

Gnomad AMR AF: 0.193

Gnomad ASJ AF: 0.206

Gnomad EAS AF: 0.0558

Gnomad SAS AF: 0.109

Gnomad FIN AF: 0.231

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.268

Gnomad OTH AF: 0.206

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

GnomAD4 genome AF: 0.200 AC: 30500 AN: 152176 Hom.: 3576 Cov.: 32 AF XY: 0.194 AC XY: 14446 AN XY: 74402

Gnomad4 AFR AF: 0.110

Gnomad4 AMR AF: 0.193

Gnomad4 ASJ AF: 0.206

Gnomad4 EAS AF: 0.0560

Gnomad4 SAS AF: 0.109

Gnomad4 FIN AF: 0.231

Gnomad4 NFE AF: 0.268

Gnomad4 OTH AF: 0.205

Alfa AF: 0.251 Hom.: 8860

Bravo AF: 0.199

Asia WGS AF: 0.0840 AC: 293 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.8
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1634718; hg19: chr6-30972865;