4-141788570-T-C

Variant names:

• chr4-141788570-T-C
• rs17007695

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 0.0839 in 151,814 control chromosomes in the GnomAD database, including 1,179 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 0.084 (1179 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.151
• Publications: 24 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 (EAS) allele frequency at 95% confidence interval = 0.396 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: 0.0840 AC: 12739 AN: 151722 Hom.: 1175 Cov.: 32

Gnomad AFR AF: 0.0217

Gnomad AMI AF: 0.0384

Gnomad AMR AF: 0.233

Gnomad ASJ AF: 0.0329

Gnomad EAS AF: 0.411

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.0851

Gnomad MID AF: 0.0649

Gnomad NFE AF: 0.0645

Gnomad OTH AF: 0.0737

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

GnomAD4 genome AF: 0.0839 AC: 12743 AN: 151814 Hom.: 1179 Cov.: 32 AF XY: 0.0900 AC XY: 6679 AN XY: 74198

African (AFR) AF: 0.0217 AC: 899 AN: 41494

American (AMR) AF: 0.233 AC: 3541 AN: 15200

Ashkenazi Jewish (ASJ) AF: 0.0329 AC: 114 AN: 3470

East Asian (EAS) AF: 0.411 AC: 2122 AN: 5164

South Asian (SAS) AF: 0.121 AC: 582 AN: 4816

European-Finnish (FIN) AF: 0.0851 AC: 887 AN: 10422

Middle Eastern (MID) AF: 0.0739 AC: 21 AN: 284

European-Non Finnish (NFE) AF: 0.0645 AC: 4381 AN: 67944

Other (OTH) AF: 0.0764 AC: 161 AN: 2108

Alfa AF: 0.0842 Hom.: 1743

Bravo AF: 0.0967

Asia WGS AF: 0.215 AC: 747 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	8.5
DANN	Benign	0.88
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs17007695; hg19: chr4-142709723;