rs4244944

Variant names:

• chr10-84085058-C-A
• rs4244944

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 0.316 in 151,970 control chromosomes in the GnomAD database, including 8,067 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 0.32 (8067 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.12
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.373 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: 0.316 AC: 48046 AN: 151852 Hom.: 8065 Cov.: 32

Gnomad AFR AF: 0.254

Gnomad AMI AF: 0.253

Gnomad AMR AF: 0.257

Gnomad ASJ AF: 0.435

Gnomad EAS AF: 0.110

Gnomad SAS AF: 0.307

Gnomad FIN AF: 0.321

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.377

Gnomad OTH AF: 0.346

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

GnomAD4 genome AF: 0.316 AC: 48076 AN: 151970 Hom.: 8067 Cov.: 32 AF XY: 0.310 AC XY: 23037 AN XY: 74290

African (AFR) AF: 0.254 AC: 10536 AN: 41452

American (AMR) AF: 0.257 AC: 3918 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.435 AC: 1508 AN: 3470

East Asian (EAS) AF: 0.111 AC: 571 AN: 5164

South Asian (SAS) AF: 0.308 AC: 1482 AN: 4806

European-Finnish (FIN) AF: 0.321 AC: 3395 AN: 10562

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.377 AC: 25601 AN: 67938

Other (OTH) AF: 0.345 AC: 729 AN: 2110

Alfa AF: 0.357 Hom.: 42141

Bravo AF: 0.308

Asia WGS AF: 0.202 AC: 702 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	13
DANN	Benign	0.65
PhyloP100		2.1

Splicing

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

Other links and lift over

dbSNP: rs4244944; hg19: chr10-85844814;