rs10942891

Variant names:

• chr5-79518420-C-G
• rs10942891

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 0.222 in 152,022 control chromosomes in the GnomAD database, including 3,941 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 0.22 (3941 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.135
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.277 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: 0.222 AC: 33769 AN: 151904 Hom.: 3939 Cov.: 32

Gnomad AFR AF: 0.281

Gnomad AMI AF: 0.311

Gnomad AMR AF: 0.182

Gnomad ASJ AF: 0.178

Gnomad EAS AF: 0.273

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.249

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.195

Gnomad OTH AF: 0.203

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

GnomAD4 genome AF: 0.222 AC: 33793 AN: 152022 Hom.: 3941 Cov.: 32 AF XY: 0.225 AC XY: 16751 AN XY: 74290

African (AFR) AF: 0.281 AC: 11667 AN: 41480

American (AMR) AF: 0.181 AC: 2771 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.178 AC: 616 AN: 3464

East Asian (EAS) AF: 0.274 AC: 1417 AN: 5172

South Asian (SAS) AF: 0.144 AC: 695 AN: 4820

European-Finnish (FIN) AF: 0.249 AC: 2630 AN: 10542

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.195 AC: 13238 AN: 67956

Other (OTH) AF: 0.203 AC: 430 AN: 2114

Alfa AF: 0.211 Hom.: 454

Bravo AF: 0.223

Asia WGS AF: 0.193 AC: 675 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	2.0
DANN	Benign	0.66
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs10942891; hg19: chr5-78814243;