rs10737175

Variant names:

• chr1-159750152-T-C
• rs10737175
• ENST00000751880.1:n.325-6918A>G

Variant summary

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

The ENST00000751880.1(ENSG00000297934):​n.325-6918A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.253 in 152,134 control chromosomes in the GnomAD database, including 5,721 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 0.25 (5721 hom., cov: 32)
• Consequence: ENSG00000297934 ENST00000751880.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.341
• Publications: 4 publications found

Genes affected

ENSG00000297934 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.733 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
ENSG00000297934	ENST00000751880.1	n.325-6918A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.253 AC: 38496 AN: 152016 Hom.: 5721 Cov.: 32

Gnomad AFR AF: 0.166

Gnomad AMI AF: 0.167

Gnomad AMR AF: 0.298

Gnomad ASJ AF: 0.337

Gnomad EAS AF: 0.753

Gnomad SAS AF: 0.325

Gnomad FIN AF: 0.223

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.254

Gnomad OTH AF: 0.283

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

GnomAD4 genome AF: 0.253 AC: 38502 AN: 152134 Hom.: 5721 Cov.: 32 AF XY: 0.255 AC XY: 18993 AN XY: 74386

African (AFR) AF: 0.166 AC: 6875 AN: 41522

American (AMR) AF: 0.298 AC: 4556 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.337 AC: 1169 AN: 3466

East Asian (EAS) AF: 0.753 AC: 3886 AN: 5164

South Asian (SAS) AF: 0.325 AC: 1567 AN: 4828

European-Finnish (FIN) AF: 0.223 AC: 2359 AN: 10594

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.254 AC: 17269 AN: 67966

Other (OTH) AF: 0.285 AC: 603 AN: 2114

Alfa AF: 0.253 Hom.: 1745

Bravo AF: 0.255

Asia WGS AF: 0.495 AC: 1718 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.7
DANN	Benign	0.74
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs10737175; hg19: chr1-159719942;