rs2420936

Variant names:

• chr10-121449367-G-A
• rs2420936

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 0.436 in 151,816 control chromosomes in the GnomAD database, including 15,274 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 0.44 (15274 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.27
• Publications: 12 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.57 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: 0.436 AC: 66210 AN: 151698 Hom.: 15263 Cov.: 31

Gnomad AFR AF: 0.307

Gnomad AMI AF: 0.449

Gnomad AMR AF: 0.580

Gnomad ASJ AF: 0.443

Gnomad EAS AF: 0.236

Gnomad SAS AF: 0.315

Gnomad FIN AF: 0.528

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.491

Gnomad OTH AF: 0.457

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

GnomAD4 genome AF: 0.436 AC: 66234 AN: 151816 Hom.: 15274 Cov.: 31 AF XY: 0.438 AC XY: 32485 AN XY: 74166

African (AFR) AF: 0.307 AC: 12701 AN: 41382

American (AMR) AF: 0.580 AC: 8858 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.443 AC: 1534 AN: 3464

East Asian (EAS) AF: 0.236 AC: 1217 AN: 5148

South Asian (SAS) AF: 0.316 AC: 1517 AN: 4802

European-Finnish (FIN) AF: 0.528 AC: 5549 AN: 10514

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.491 AC: 33363 AN: 67926

Other (OTH) AF: 0.452 AC: 955 AN: 2112

Alfa AF: 0.477 Hom.: 56772

Bravo AF: 0.439

Asia WGS AF: 0.289 AC: 1003 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	7.4
DANN	Benign	0.58
PhyloP100		2.3

Splicing

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

Other links and lift over

dbSNP: rs2420936; hg19: chr10-123208881;