rs2031621

chr10-106356319-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 0.297 in 152,078 control chromosomes in the GnomAD database, including 7,495 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 0.30 (7495 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0990

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.379 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: 0.297 AC: 45134 AN: 151960 Hom.: 7494 Cov.: 33

Gnomad AFR AF: 0.160

Gnomad AMI AF: 0.368

Gnomad AMR AF: 0.308

Gnomad ASJ AF: 0.298

Gnomad EAS AF: 0.119

Gnomad SAS AF: 0.299

Gnomad FIN AF: 0.333

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.383

Gnomad OTH AF: 0.348

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

GnomAD4 genome AF: 0.297 AC: 45146 AN: 152078 Hom.: 7495 Cov.: 33 AF XY: 0.295 AC XY: 21942 AN XY: 74356

Gnomad4 AFR AF: 0.160

Gnomad4 AMR AF: 0.308

Gnomad4 ASJ AF: 0.298

Gnomad4 EAS AF: 0.118

Gnomad4 SAS AF: 0.301

Gnomad4 FIN AF: 0.333

Gnomad4 NFE AF: 0.383

Gnomad4 OTH AF: 0.345

Alfa AF: 0.367 Hom.: 21679

Bravo AF: 0.287

Asia WGS AF: 0.188 AC: 655 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.71
Dann	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2031621; hg19: chr10-108116077;