rs2437935

Positions:

• chr10-44256820-G-A
• chr10-44256820-G-T

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 0.522 in 151,996 control chromosomes in the GnomAD database, including 22,827 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 0.52 (22827 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0450

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 = 0.643 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: 0.522 AC: 79266 AN: 151878 Hom.: 22828 Cov.: 32

Gnomad AFR AF: 0.264

Gnomad AMI AF: 0.720

Gnomad AMR AF: 0.555

Gnomad ASJ AF: 0.601

Gnomad EAS AF: 0.528

Gnomad SAS AF: 0.481

Gnomad FIN AF: 0.640

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.649

Gnomad OTH AF: 0.532

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

GnomAD4 genome AF: 0.522 AC: 79272 AN: 151996 Hom.: 22827 Cov.: 32 AF XY: 0.521 AC XY: 38679 AN XY: 74282

Gnomad4 AFR AF: 0.263

Gnomad4 AMR AF: 0.554

Gnomad4 ASJ AF: 0.601

Gnomad4 EAS AF: 0.527

Gnomad4 SAS AF: 0.480

Gnomad4 FIN AF: 0.640

Gnomad4 NFE AF: 0.649

Gnomad4 OTH AF: 0.537

Alfa AF: 0.598 Hom.: 15656

Bravo AF: 0.504

Asia WGS AF: 0.536 AC: 1865 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.67
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2437935; hg19: chr10-44752268;