rs10915437

Variant names:

• chr1-4122946-A-G
• rs10915437

Your query was ambiguous. Multiple possible variants found:

• chr1-4122946-A-G
• chr1-4122946-A-T

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 0.296 in 152,154 control chromosomes in the GnomAD database, including 7,532 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 (7532 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.356
• Publications: 18 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 = 0.365 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: 0.296 AC: 45062 AN: 152036 Hom.: 7525 Cov.: 33

Gnomad AFR AF: 0.131

Gnomad AMI AF: 0.479

Gnomad AMR AF: 0.344

Gnomad ASJ AF: 0.366

Gnomad EAS AF: 0.323

Gnomad SAS AF: 0.341

Gnomad FIN AF: 0.339

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.369

Gnomad OTH AF: 0.299

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

GnomAD4 genome AF: 0.296 AC: 45077 AN: 152154 Hom.: 7532 Cov.: 33 AF XY: 0.298 AC XY: 22198 AN XY: 74394

African (AFR) AF: 0.131 AC: 5423 AN: 41530

American (AMR) AF: 0.344 AC: 5254 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.366 AC: 1270 AN: 3468

East Asian (EAS) AF: 0.323 AC: 1665 AN: 5158

South Asian (SAS) AF: 0.340 AC: 1642 AN: 4828

European-Finnish (FIN) AF: 0.339 AC: 3590 AN: 10588

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.369 AC: 25083 AN: 67974

Other (OTH) AF: 0.305 AC: 645 AN: 2112

Alfa AF: 0.331 Hom.: 13470

Bravo AF: 0.289

Asia WGS AF: 0.340 AC: 1184 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.6
DANN	Benign	0.45
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs10915437; hg19: chr1-4183006;