chr4-41988273-C-T

Variant names:

• chr4-41988273-C-T
• rs2581435

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 0.64 in 152,064 control chromosomes in the GnomAD database, including 35,764 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 0.64 (35764 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0370
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.94 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: 0.640 AC: 97247 AN: 151948 Hom.: 35756 Cov.: 32

Gnomad AFR AF: 0.248

Gnomad AMI AF: 0.913

Gnomad AMR AF: 0.764

Gnomad ASJ AF: 0.709

Gnomad EAS AF: 0.962

Gnomad SAS AF: 0.812

Gnomad FIN AF: 0.824

Gnomad MID AF: 0.684

Gnomad NFE AF: 0.777

Gnomad OTH AF: 0.659

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

GnomAD4 genome AF: 0.640 AC: 97275 AN: 152064 Hom.: 35764 Cov.: 32 AF XY: 0.649 AC XY: 48202 AN XY: 74322

African (AFR) AF: 0.248 AC: 10268 AN: 41430

American (AMR) AF: 0.765 AC: 11680 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.709 AC: 2460 AN: 3470

East Asian (EAS) AF: 0.962 AC: 4988 AN: 5184

South Asian (SAS) AF: 0.812 AC: 3906 AN: 4812

European-Finnish (FIN) AF: 0.824 AC: 8731 AN: 10596

Middle Eastern (MID) AF: 0.684 AC: 201 AN: 294

European-Non Finnish (NFE) AF: 0.777 AC: 52808 AN: 67978

Other (OTH) AF: 0.662 AC: 1400 AN: 2114

Alfa AF: 0.673 Hom.: 4887

Bravo AF: 0.620

Asia WGS AF: 0.843 AC: 2921 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	1.3
DANN	Benign	0.63
PhyloP100		-0.037

Splicing

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

Other links and lift over

dbSNP: rs2581435; hg19: chr4-41990290;