chr10-72089881-G-A

Variant names:

• chr10-72089881-G-A
• rs1245541

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 0.357 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
• Publications: 20 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.318 AC: 13169 AN: 41438

American (AMR) AF: 0.354 AC: 5405 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.380 AC: 1319 AN: 3470

East Asian (EAS) AF: 0.137 AC: 711 AN: 5186

South Asian (SAS) AF: 0.396 AC: 1908 AN: 4818

European-Finnish (FIN) AF: 0.318 AC: 3362 AN: 10572

Middle Eastern (MID) AF: 0.408 AC: 120 AN: 294

European-Non Finnish (NFE) AF: 0.399 AC: 27150 AN: 67966

Other (OTH) AF: 0.368 AC: 778 AN: 2112

Alfa AF: 0.378 Hom.: 20790

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
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs1245541; hg19: chr10-73849639;