rs34787256

Variant names:

• chr1-207319994-C-T
• rs34787256
• ENST00000740658.1:n.116+1692G>A

Variant summary

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

The ENST00000740658.1(ENSG00000296591):​n.116+1692G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0147 in 152,226 control chromosomes in the GnomAD database, including 21 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 0.015 (21 hom., cov: 31)
• Consequence: ENSG00000296591 ENST00000740658.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.683
• Publications: 0 publications found

Genes affected

ENSG00000296591 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0147 (2235/152226) while in subpopulation NFE AF = 0.0205 (1397/67992). AF 95% confidence interval is 0.0197. There are 21 homozygotes in GnomAd4. There are 1107 alleles in the male GnomAd4 subpopulation. Median coverage is 31. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 21 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107985251	XR_007066837.1	n.444+1692G>A		intron_variant	Intron 1 of 3
LOC107985251	XR_007066838.1	n.444+1692G>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000296591	ENST00000740658.1	n.116+1692G>A		intron_variant	Intron 1 of 2
ENSG00000296591	ENST00000740659.1	n.96+1692G>A		intron_variant	Intron 1 of 4
ENSG00000296591	ENST00000740660.1	n.89+1692G>A		intron_variant	Intron 1 of 3
ENSG00000296591	ENST00000740661.1	n.86+1692G>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.0147 AC: 2233 AN: 152108 Hom.: 21 Cov.: 31

Gnomad AFR AF: 0.00341

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.0145

Gnomad ASJ AF: 0.00749

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00249

Gnomad FIN AF: 0.0364

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0205

Gnomad OTH AF: 0.0167

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

GnomAD4 genome AF: 0.0147 AC: 2235 AN: 152226 Hom.: 21 Cov.: 31 AF XY: 0.0149 AC XY: 1107 AN XY: 74436

African (AFR) AF: 0.00340 AC: 141 AN: 41530

American (AMR) AF: 0.0144 AC: 221 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.00749 AC: 26 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5186

South Asian (SAS) AF: 0.00249 AC: 12 AN: 4818

European-Finnish (FIN) AF: 0.0364 AC: 386 AN: 10610

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0205 AC: 1397 AN: 67992

Other (OTH) AF: 0.0165 AC: 35 AN: 2116

Alfa AF: 0.0163 Hom.: 3

Bravo AF: 0.0130

Asia WGS AF: 0.00202 AC: 7 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.16
DANN	Benign	0.63
PhyloP100		-0.68

Splicing

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

Other links and lift over

dbSNP: rs34787256; hg19: chr1-207493339;