rs1245541

Positions:

• chr10-72089881-G-A

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 0.357 in 152,038 control chromosomes in the GnomAD database, including 10,031 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 0.36 (10031 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.43

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.395 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.357 AC: 54308 AN: 151920 Hom.: 10027 Cov.: 32

Gnomad AFR AF: 0.318

Gnomad AMI AF: 0.441

Gnomad AMR AF: 0.355

Gnomad ASJ AF: 0.380

Gnomad EAS AF: 0.138

Gnomad SAS AF: 0.395

Gnomad FIN AF: 0.318

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.399

Gnomad OTH AF: 0.373

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

GnomAD4 genome AF: 0.357 AC: 54323 AN: 152038 Hom.: 10031 Cov.: 32 AF XY: 0.352 AC XY: 26147 AN XY: 74338

Gnomad4 AFR AF: 0.318

Gnomad4 AMR AF: 0.354

Gnomad4 ASJ AF: 0.380

Gnomad4 EAS AF: 0.137

Gnomad4 SAS AF: 0.396

Gnomad4 FIN AF: 0.318

Gnomad4 NFE AF: 0.399

Gnomad4 OTH AF: 0.368

Alfa AF: 0.383 Hom.: 13630

Bravo AF: 0.356

Asia WGS AF: 0.228 AC: 796 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.28
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1245541; hg19: chr10-73849639;