rs10865170

Variant names:

• chr2-41534660-C-A
• rs10865170
• ENST00000775670.1:n.74+3066G>T

Variant summary

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

The ENST00000775670.1(ENSG00000301031):​n.74+3066G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.326 in 151,974 control chromosomes in the GnomAD database, including 8,939 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 0.33 (8939 hom., cov: 32)
• Consequence: ENSG00000301031 ENST00000775670.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.148
• Publications: 5 publications found

Genes affected

ENSG00000301031 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.7 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105374506	XR_939997.3	n.9529+3066G>T		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000301031	ENST00000775670.1	n.74+3066G>T		intron_variant	Intron 1 of 2
ENSG00000301031	ENST00000775672.1	n.74+3066G>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.326 AC: 49480 AN: 151856 Hom.: 8905 Cov.: 32

Gnomad AFR AF: 0.353

Gnomad AMI AF: 0.122

Gnomad AMR AF: 0.459

Gnomad ASJ AF: 0.243

Gnomad EAS AF: 0.719

Gnomad SAS AF: 0.345

Gnomad FIN AF: 0.337

Gnomad MID AF: 0.318

Gnomad NFE AF: 0.254

Gnomad OTH AF: 0.316

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

GnomAD4 genome AF: 0.326 AC: 49549 AN: 151974 Hom.: 8939 Cov.: 32 AF XY: 0.332 AC XY: 24655 AN XY: 74282

African (AFR) AF: 0.353 AC: 14628 AN: 41420

American (AMR) AF: 0.460 AC: 7024 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.243 AC: 841 AN: 3468

East Asian (EAS) AF: 0.719 AC: 3703 AN: 5150

South Asian (SAS) AF: 0.345 AC: 1662 AN: 4812

European-Finnish (FIN) AF: 0.337 AC: 3563 AN: 10566

Middle Eastern (MID) AF: 0.322 AC: 94 AN: 292

European-Non Finnish (NFE) AF: 0.254 AC: 17238 AN: 67966

Other (OTH) AF: 0.325 AC: 685 AN: 2110

Alfa AF: 0.297 Hom.: 924

Bravo AF: 0.340

Asia WGS AF: 0.529 AC: 1838 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.4
DANN	Benign	0.53
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs10865170; hg19: chr2-41761800;