10-106356319-G-A

Variant names:

• chr10-106356319-G-A
• rs2031621

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.160 AC: 6644 AN: 41516

American (AMR) AF: 0.308 AC: 4710 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.298 AC: 1036 AN: 3472

East Asian (EAS) AF: 0.118 AC: 611 AN: 5176

South Asian (SAS) AF: 0.301 AC: 1453 AN: 4826

European-Finnish (FIN) AF: 0.333 AC: 3511 AN: 10546

Middle Eastern (MID) AF: 0.404 AC: 118 AN: 292

European-Non Finnish (NFE) AF: 0.383 AC: 25998 AN: 67942

Other (OTH) AF: 0.345 AC: 729 AN: 2112

Alfa AF: 0.354 Hom.: 42373

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
PhyloP100		0.099

Splicing

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

Other links and lift over

dbSNP: rs2031621; hg19: chr10-108116077;