3-178048676-T-G

Variant names:

• chr3-178048676-T-G
• rs7634528
• ENST00000651726.1:n.235-17771A>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000651726.1(ENSG00000286003):​n.235-17771A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0409 in 152,218 control chromosomes in the GnomAD database, including 128 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 0.041 (128 hom., cov: 32)
• Consequence: ENSG00000286003 ENST00000651726.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36
• Publications: 5 publications found

Genes affected

ENSG00000286003 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.0409 (6226/152218) while in subpopulation AFR AF = 0.0501 (2082/41528). AF 95% confidence interval is 0.0483. There are 128 homozygotes in GnomAd4. There are 2883 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 128 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105374234	XR_001741026.1	n.115-1379T>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286003	ENST00000651726.1	n.235-17771A>C		intron_variant	Intron 1 of 3
ENSG00000301516	ENST00000779445.1	n.213-248T>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.0410 AC: 6229 AN: 152100 Hom.: 127 Cov.: 32

Gnomad AFR AF: 0.0503

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0286

Gnomad ASJ AF: 0.0530

Gnomad EAS AF: 0.000962

Gnomad SAS AF: 0.0139

Gnomad FIN AF: 0.0209

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0463

Gnomad OTH AF: 0.0354

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

GnomAD4 genome AF: 0.0409 AC: 6226 AN: 152218 Hom.: 128 Cov.: 32 AF XY: 0.0387 AC XY: 2883 AN XY: 74442

African (AFR) AF: 0.0501 AC: 2082 AN: 41528

American (AMR) AF: 0.0286 AC: 436 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0530 AC: 184 AN: 3472

East Asian (EAS) AF: 0.000965 AC: 5 AN: 5184

South Asian (SAS) AF: 0.0137 AC: 66 AN: 4828

European-Finnish (FIN) AF: 0.0209 AC: 222 AN: 10618

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0463 AC: 3148 AN: 68002

Other (OTH) AF: 0.0351 AC: 74 AN: 2110

Alfa AF: 0.0425 Hom.: 440

Bravo AF: 0.0417

Asia WGS AF: 0.00808 AC: 29 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.18
DANN	Benign	0.63
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs7634528; hg19: chr3-177766464;