4-69876444-T-C

Variant names:

• chr4-69876444-T-C
• rs1529041

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.106

Gnomad4 AMR AF: 0.336

Gnomad4 ASJ AF: 0.283

Gnomad4 EAS AF: 0.206

Gnomad4 SAS AF: 0.438

Gnomad4 FIN AF: 0.264

Gnomad4 NFE AF: 0.299

Gnomad4 OTH AF: 0.261

Alfa AF: 0.160 Hom.: 357

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1529041; hg19: chr4-70742162;