chr2-41534660-C-A

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000775670.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000301031	ENST00000775670.1		n.74+3066G>T		intron	N/A
	ENSG00000301031	ENST00000775672.1		n.74+3066G>T		intron	N/A

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 v4.9

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;