chr4-147368237-T-C

Variant names:

• chr4-147368237-T-C
• rs1429142

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 0.335 in 152,124 control chromosomes in the GnomAD database, including 12,653 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 0.33 (12653 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.967
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.692 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: 0.335 AC: 50858 AN: 152004 Hom.: 12620 Cov.: 32

Gnomad AFR AF: 0.699

Gnomad AMI AF: 0.188

Gnomad AMR AF: 0.257

Gnomad ASJ AF: 0.174

Gnomad EAS AF: 0.343

Gnomad SAS AF: 0.352

Gnomad FIN AF: 0.148

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.169

Gnomad OTH AF: 0.305

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

GnomAD4 genome AF: 0.335 AC: 50945 AN: 152124 Hom.: 12653 Cov.: 32 AF XY: 0.333 AC XY: 24751 AN XY: 74414

African (AFR) AF: 0.699 AC: 28974 AN: 41470

American (AMR) AF: 0.257 AC: 3929 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.174 AC: 604 AN: 3470

East Asian (EAS) AF: 0.344 AC: 1775 AN: 5166

South Asian (SAS) AF: 0.352 AC: 1695 AN: 4822

European-Finnish (FIN) AF: 0.148 AC: 1568 AN: 10610

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.169 AC: 11512 AN: 67982

Other (OTH) AF: 0.310 AC: 654 AN: 2112

Alfa AF: 0.220 Hom.: 21936

Bravo AF: 0.357

Asia WGS AF: 0.403 AC: 1405 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.16
DANN	Benign	0.55
PhyloP100		-0.97

Splicing

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

Other links and lift over

dbSNP: rs1429142; hg19: chr4-148289389;