chr4-178189362-A-G

Variant names:

• chr4-178189362-A-G
• rs2378811

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 0.411 in 151,928 control chromosomes in the GnomAD database, including 13,297 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 0.41 (13297 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.266
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.563 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: 0.411 AC: 62441 AN: 151810 Hom.: 13290 Cov.: 31

Gnomad AFR AF: 0.318

Gnomad AMI AF: 0.557

Gnomad AMR AF: 0.519

Gnomad ASJ AF: 0.410

Gnomad EAS AF: 0.580

Gnomad SAS AF: 0.451

Gnomad FIN AF: 0.399

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.427

Gnomad OTH AF: 0.444

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

GnomAD4 genome AF: 0.411 AC: 62478 AN: 151928 Hom.: 13297 Cov.: 31 AF XY: 0.415 AC XY: 30795 AN XY: 74274

African (AFR) AF: 0.318 AC: 13165 AN: 41444

American (AMR) AF: 0.520 AC: 7931 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.410 AC: 1423 AN: 3470

East Asian (EAS) AF: 0.580 AC: 2981 AN: 5136

South Asian (SAS) AF: 0.450 AC: 2167 AN: 4820

European-Finnish (FIN) AF: 0.399 AC: 4197 AN: 10530

Middle Eastern (MID) AF: 0.439 AC: 129 AN: 294

European-Non Finnish (NFE) AF: 0.427 AC: 29036 AN: 67956

Other (OTH) AF: 0.448 AC: 942 AN: 2104

Alfa AF: 0.434 Hom.: 2480

Bravo AF: 0.417

Asia WGS AF: 0.540 AC: 1878 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.27
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs2378811; hg19: chr4-179110516;