rs7634528

Positions:

• chr3-178048676-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000651726.1(ENSG00000286003):​n.235-17771A>C variant causes a intron, non coding transcript 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: ENST00000651726.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 128 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105374234	XR_001741026.1	n.115-1379T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000651726.1	n.235-17771A>C		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.0501

Gnomad4 AMR AF: 0.0286

Gnomad4 ASJ AF: 0.0530

Gnomad4 EAS AF: 0.000965

Gnomad4 SAS AF: 0.0137

Gnomad4 FIN AF: 0.0209

Gnomad4 NFE AF: 0.0463

Gnomad4 OTH AF: 0.0351

Alfa AF: 0.0425 Hom.: 173

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7634528; hg19: chr3-177766464;