rs1634718

Positions:

• chr6-31005088-A-G

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;