rs4948876

Variant names:

• chr10-44361298-A-T
• rs4948876

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 0.148 in 152,254 control chromosomes in the GnomAD database, including 2,001 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 0.15 (2001 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.384
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.177 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: 0.149 AC: 22609 AN: 152136 Hom.: 2004 Cov.: 33

Gnomad AFR AF: 0.0536

Gnomad AMI AF: 0.103

Gnomad AMR AF: 0.177

Gnomad ASJ AF: 0.144

Gnomad EAS AF: 0.173

Gnomad SAS AF: 0.189

Gnomad FIN AF: 0.276

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.176

Gnomad OTH AF: 0.162

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

GnomAD4 genome AF: 0.148 AC: 22597 AN: 152254 Hom.: 2001 Cov.: 33 AF XY: 0.156 AC XY: 11597 AN XY: 74430

African (AFR) AF: 0.0534 AC: 2222 AN: 41572

American (AMR) AF: 0.177 AC: 2703 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.144 AC: 499 AN: 3470

East Asian (EAS) AF: 0.173 AC: 895 AN: 5178

South Asian (SAS) AF: 0.187 AC: 904 AN: 4828

European-Finnish (FIN) AF: 0.276 AC: 2921 AN: 10588

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.176 AC: 11976 AN: 68002

Other (OTH) AF: 0.161 AC: 340 AN: 2112

Alfa AF: 0.162 Hom.: 270

Bravo AF: 0.136

Asia WGS AF: 0.168 AC: 584 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.4
DANN	Benign	0.75
PhyloP100		0.38
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs4948876; hg19: chr10-44856746;