4-177396798-C-T

Variant names:

• chr4-177396798-C-T
• rs1395477

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 0.436 in 152,014 control chromosomes in the GnomAD database, including 15,740 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 0.44 (15740 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.405
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.59 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: 0.436 AC: 66201 AN: 151898 Hom.: 15736 Cov.: 32

Gnomad AFR AF: 0.235

Gnomad AMI AF: 0.549

Gnomad AMR AF: 0.437

Gnomad ASJ AF: 0.543

Gnomad EAS AF: 0.466

Gnomad SAS AF: 0.608

Gnomad FIN AF: 0.393

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.542

Gnomad OTH AF: 0.457

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

GnomAD4 genome AF: 0.436 AC: 66208 AN: 152014 Hom.: 15740 Cov.: 32 AF XY: 0.434 AC XY: 32242 AN XY: 74276

African (AFR) AF: 0.234 AC: 9730 AN: 41494

American (AMR) AF: 0.437 AC: 6671 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.543 AC: 1887 AN: 3472

East Asian (EAS) AF: 0.466 AC: 2404 AN: 5162

South Asian (SAS) AF: 0.608 AC: 2930 AN: 4816

European-Finnish (FIN) AF: 0.393 AC: 4143 AN: 10546

Middle Eastern (MID) AF: 0.497 AC: 143 AN: 288

European-Non Finnish (NFE) AF: 0.542 AC: 36841 AN: 67942

Other (OTH) AF: 0.455 AC: 959 AN: 2108

Alfa AF: 0.517 Hom.: 21697

Bravo AF: 0.428

Asia WGS AF: 0.475 AC: 1653 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	6.0
DANN	Benign	0.43
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs1395477; hg19: chr4-178317952;