4-69876444-T-C

Variant names:

• chr4-69876444-T-C
• rs1529041

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 0.247 in 151,796 control chromosomes in the GnomAD database, including 5,341 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 0.25 (5341 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.72
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.423 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: 0.247 AC: 37514 AN: 151676 Hom.: 5340 Cov.: 31

Gnomad AFR AF: 0.107

Gnomad AMI AF: 0.154

Gnomad AMR AF: 0.336

Gnomad ASJ AF: 0.283

Gnomad EAS AF: 0.205

Gnomad SAS AF: 0.438

Gnomad FIN AF: 0.264

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.299

Gnomad OTH AF: 0.262

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

GnomAD4 genome AF: 0.247 AC: 37523 AN: 151796 Hom.: 5341 Cov.: 31 AF XY: 0.249 AC XY: 18485 AN XY: 74160

African (AFR) AF: 0.106 AC: 4404 AN: 41404

American (AMR) AF: 0.336 AC: 5105 AN: 15196

Ashkenazi Jewish (ASJ) AF: 0.283 AC: 981 AN: 3472

East Asian (EAS) AF: 0.206 AC: 1055 AN: 5130

South Asian (SAS) AF: 0.438 AC: 2110 AN: 4812

European-Finnish (FIN) AF: 0.264 AC: 2785 AN: 10548

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.299 AC: 20317 AN: 67914

Other (OTH) AF: 0.261 AC: 552 AN: 2114

Alfa AF: 0.158 Hom.: 361

Bravo AF: 0.244

Asia WGS AF: 0.296 AC: 1028 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.5
DANN	Benign	0.46
PhyloP100		1.7

Splicing

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

Other links and lift over

dbSNP: rs1529041; hg19: chr4-70742162;