4-178634603-T-C

Variant names:

• chr4-178634603-T-C
• rs1368870

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 0.361 in 152,084 control chromosomes in the GnomAD database, including 11,853 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 0.36 (11853 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.735

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.486 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: 0.361 AC: 54819 AN: 151966 Hom.: 11842 Cov.: 32

Gnomad AFR AF: 0.155

Gnomad AMI AF: 0.650

Gnomad AMR AF: 0.314

Gnomad ASJ AF: 0.449

Gnomad EAS AF: 0.0150

Gnomad SAS AF: 0.451

Gnomad FIN AF: 0.471

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.491

Gnomad OTH AF: 0.378

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

GnomAD4 genome AF: 0.361 AC: 54852 AN: 152084 Hom.: 11853 Cov.: 32 AF XY: 0.356 AC XY: 26497 AN XY: 74338

Gnomad4 AFR AF: 0.155

Gnomad4 AMR AF: 0.313

Gnomad4 ASJ AF: 0.449

Gnomad4 EAS AF: 0.0153

Gnomad4 SAS AF: 0.452

Gnomad4 FIN AF: 0.471

Gnomad4 NFE AF: 0.491

Gnomad4 OTH AF: 0.376

Alfa AF: 0.309 Hom.: 957

Bravo AF: 0.334

Asia WGS AF: 0.226 AC: 788 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	9.3
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1368870; hg19: chr4-179555757;