rs1467616

Variant names:

• chr10-100881934-G-A
• rs1467616

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 0.597 in 152,148 control chromosomes in the GnomAD database, including 27,643 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 0.60 (27643 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0510

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.652 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: 0.597 AC: 90750 AN: 152030 Hom.: 27631 Cov.: 33

Gnomad AFR AF: 0.498

Gnomad AMI AF: 0.672

Gnomad AMR AF: 0.634

Gnomad ASJ AF: 0.663

Gnomad EAS AF: 0.343

Gnomad SAS AF: 0.579

Gnomad FIN AF: 0.641

Gnomad MID AF: 0.752

Gnomad NFE AF: 0.657

Gnomad OTH AF: 0.617

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

GnomAD4 genome AF: 0.597 AC: 90800 AN: 152148 Hom.: 27643 Cov.: 33 AF XY: 0.594 AC XY: 44204 AN XY: 74368

Gnomad4 AFR AF: 0.498

Gnomad4 AMR AF: 0.634

Gnomad4 ASJ AF: 0.663

Gnomad4 EAS AF: 0.343

Gnomad4 SAS AF: 0.580

Gnomad4 FIN AF: 0.641

Gnomad4 NFE AF: 0.657

Gnomad4 OTH AF: 0.614

Alfa AF: 0.646 Hom.: 43286

Bravo AF: 0.589

Asia WGS AF: 0.474 AC: 1648 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.34
DANN	Benign	0.16

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1467616; hg19: chr10-102641691;