4-178634603-T-C

Variant names:

• chr4-178634603-T-C
• rs1368870

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 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
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.486 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.155 AC: 6441 AN: 41520

American (AMR) AF: 0.313 AC: 4784 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.449 AC: 1556 AN: 3468

East Asian (EAS) AF: 0.0153 AC: 79 AN: 5180

South Asian (SAS) AF: 0.452 AC: 2183 AN: 4826

European-Finnish (FIN) AF: 0.471 AC: 4972 AN: 10564

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

European-Non Finnish (NFE) AF: 0.491 AC: 33339 AN: 67956

Other (OTH) AF: 0.376 AC: 794 AN: 2112

Alfa AF: 0.300 Hom.: 968

Bravo AF: 0.334

Asia WGS AF: 0.226 AC: 788 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	9.3
DANN	Benign	0.80
PhyloP100		0.73

Splicing

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

Other links and lift over

dbSNP: rs1368870; hg19: chr4-179555757;