10-121651831-A-G

Variant names:

• chr10-121651831-A-G
• rs1909668

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 0.598 in 152,146 control chromosomes in the GnomAD database, including 28,017 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 (28017 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.295
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.661 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: 0.598 AC: 90978 AN: 152028 Hom.: 28013 Cov.: 34

Gnomad AFR AF: 0.431

Gnomad AMI AF: 0.808

Gnomad AMR AF: 0.666

Gnomad ASJ AF: 0.724

Gnomad EAS AF: 0.635

Gnomad SAS AF: 0.638

Gnomad FIN AF: 0.623

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.666

Gnomad OTH AF: 0.604

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

GnomAD4 genome AF: 0.598 AC: 91014 AN: 152146 Hom.: 28017 Cov.: 34 AF XY: 0.599 AC XY: 44545 AN XY: 74400

African (AFR) AF: 0.430 AC: 17854 AN: 41490

American (AMR) AF: 0.666 AC: 10180 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.724 AC: 2512 AN: 3472

East Asian (EAS) AF: 0.634 AC: 3286 AN: 5184

South Asian (SAS) AF: 0.638 AC: 3075 AN: 4822

European-Finnish (FIN) AF: 0.623 AC: 6598 AN: 10586

Middle Eastern (MID) AF: 0.616 AC: 181 AN: 294

European-Non Finnish (NFE) AF: 0.666 AC: 45307 AN: 67990

Other (OTH) AF: 0.607 AC: 1284 AN: 2114

Alfa AF: 0.637 Hom.: 14298

Bravo AF: 0.591

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.61
DANN	Benign	0.68
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs1909668; hg19: chr10-123411345;