rs41456044

Variant names:

• chr4-122825874-T-A
• rs41456044

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 0.0947 in 152,250 control chromosomes in the GnomAD database, including 1,161 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 0.095 (1161 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.903
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.206 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: 0.0946 AC: 14391 AN: 152132 Hom.: 1161 Cov.: 33

Gnomad AFR AF: 0.210

Gnomad AMI AF: 0.0614

Gnomad AMR AF: 0.0708

Gnomad ASJ AF: 0.122

Gnomad EAS AF: 0.000769

Gnomad SAS AF: 0.0858

Gnomad FIN AF: 0.0194

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.0478

Gnomad OTH AF: 0.106

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

GnomAD4 genome AF: 0.0947 AC: 14414 AN: 152250 Hom.: 1161 Cov.: 33 AF XY: 0.0928 AC XY: 6908 AN XY: 74448

African (AFR) AF: 0.210 AC: 8717 AN: 41514

American (AMR) AF: 0.0706 AC: 1081 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.122 AC: 424 AN: 3470

East Asian (EAS) AF: 0.000771 AC: 4 AN: 5190

South Asian (SAS) AF: 0.0859 AC: 414 AN: 4822

European-Finnish (FIN) AF: 0.0194 AC: 206 AN: 10622

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.0477 AC: 3247 AN: 68012

Other (OTH) AF: 0.105 AC: 221 AN: 2108

Alfa AF: 0.0759 Hom.: 87

Bravo AF: 0.104

Asia WGS AF: 0.0440 AC: 152 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.7
DANN	Benign	0.48
PhyloP100		-0.90

Splicing

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

Other links and lift over

dbSNP: rs41456044; hg19: chr4-123747029;