4-177374275-C-T

Variant names:

• chr4-177374275-C-T
• rs17739370
• XR_001741926.2:n.36+7040G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_001741926.2(LOC105377558):​n.36+7040G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.379 in 151,984 control chromosomes in the GnomAD database, including 11,146 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 0.38 (11146 hom., cov: 32)
• Consequence: LOC105377558 XR_001741926.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.156
• Publications: 6 publications found

Genes affected

LOC105377558 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.406 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: 0.380 AC: 57638 AN: 151866 Hom.: 11140 Cov.: 32

Gnomad AFR AF: 0.354

Gnomad AMI AF: 0.542

Gnomad AMR AF: 0.347

Gnomad ASJ AF: 0.329

Gnomad EAS AF: 0.230

Gnomad SAS AF: 0.331

Gnomad FIN AF: 0.432

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.410

Gnomad OTH AF: 0.365

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

GnomAD4 genome AF: 0.379 AC: 57676 AN: 151984 Hom.: 11146 Cov.: 32 AF XY: 0.377 AC XY: 28011 AN XY: 74286

African (AFR) AF: 0.354 AC: 14691 AN: 41466

American (AMR) AF: 0.346 AC: 5281 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.329 AC: 1141 AN: 3466

East Asian (EAS) AF: 0.230 AC: 1188 AN: 5166

South Asian (SAS) AF: 0.332 AC: 1600 AN: 4822

European-Finnish (FIN) AF: 0.432 AC: 4561 AN: 10548

Middle Eastern (MID) AF: 0.381 AC: 112 AN: 294

European-Non Finnish (NFE) AF: 0.410 AC: 27847 AN: 67940

Other (OTH) AF: 0.361 AC: 761 AN: 2108

Alfa AF: 0.393 Hom.: 15678

Bravo AF: 0.373

Asia WGS AF: 0.293 AC: 1024 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.1
DANN	Benign	0.46
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs17739370; hg19: chr4-178295429;