4-178634264-C-T

Variant names:

• chr4-178634264-C-T
• rs1368871

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 0.361 in 151,994 control chromosomes in the GnomAD database, including 11,831 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 (11831 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0210
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• 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: 54774 AN: 151876 Hom.: 11819 Cov.: 33

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.651

Gnomad AMR AF: 0.314

Gnomad ASJ AF: 0.449

Gnomad EAS AF: 0.0152

Gnomad SAS AF: 0.451

Gnomad FIN AF: 0.471

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.491

Gnomad OTH AF: 0.380

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

GnomAD4 genome AF: 0.361 AC: 54808 AN: 151994 Hom.: 11831 Cov.: 33 AF XY: 0.356 AC XY: 26462 AN XY: 74282

African (AFR) AF: 0.155 AC: 6421 AN: 41472

American (AMR) AF: 0.313 AC: 4776 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.449 AC: 1557 AN: 3468

East Asian (EAS) AF: 0.0154 AC: 80 AN: 5180

South Asian (SAS) AF: 0.452 AC: 2181 AN: 4824

European-Finnish (FIN) AF: 0.471 AC: 4975 AN: 10566

Middle Eastern (MID) AF: 0.395 AC: 116 AN: 294

European-Non Finnish (NFE) AF: 0.491 AC: 33318 AN: 67924

Other (OTH) AF: 0.377 AC: 794 AN: 2106

Alfa AF: 0.315 Hom.: 1048

Bravo AF: 0.334

Asia WGS AF: 0.225 AC: 784 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	5.1
DANN	Benign	0.69
PhyloP100		0.021

Splicing

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

Other links and lift over

dbSNP: rs1368871; hg19: chr4-179555418;