rs10496611

Variant names:

• chr2-123373968-G-A
• rs10496611
• ENST00000807628.1:n.107-23804C>T

Your query was ambiguous. Multiple possible variants found:

• chr2-123373968-G-A
• chr2-123373968-G-C
• chr2-123373968-G-T

Variant summary

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

The ENST00000807628.1(ENSG00000305007):​n.107-23804C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.297 in 151,866 control chromosomes in the GnomAD database, including 7,193 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 0.30 (7193 hom., cov: 32)
• Consequence: ENSG00000305007 ENST00000807628.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.118
• Publications: 1 publications found

Genes affected

ENSG00000305007 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.404 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000807628.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000305007	ENST00000807628.1		n.107-23804C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.298 AC: 45153 AN: 151748 Hom.: 7190 Cov.: 32

Gnomad AFR AF: 0.210

Gnomad AMI AF: 0.393

Gnomad AMR AF: 0.231

Gnomad ASJ AF: 0.310

Gnomad EAS AF: 0.420

Gnomad SAS AF: 0.372

Gnomad FIN AF: 0.425

Gnomad MID AF: 0.328

Gnomad NFE AF: 0.329

Gnomad OTH AF: 0.296

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

GnomAD4 genome AF: 0.297 AC: 45155 AN: 151866 Hom.: 7193 Cov.: 32 AF XY: 0.302 AC XY: 22414 AN XY: 74208

African (AFR) AF: 0.210 AC: 8690 AN: 41416

American (AMR) AF: 0.230 AC: 3512 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.310 AC: 1074 AN: 3468

East Asian (EAS) AF: 0.419 AC: 2151 AN: 5134

South Asian (SAS) AF: 0.373 AC: 1797 AN: 4816

European-Finnish (FIN) AF: 0.425 AC: 4468 AN: 10524

Middle Eastern (MID) AF: 0.346 AC: 101 AN: 292

European-Non Finnish (NFE) AF: 0.329 AC: 22386 AN: 67958

Other (OTH) AF: 0.294 AC: 618 AN: 2104

Alfa AF: 0.300 Hom.: 5308

Bravo AF: 0.278

Asia WGS AF: 0.350 AC: 1217 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.2
DANN	Benign	0.85
PhyloP100		-0.12

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10496611;

hg19: chr2-124131544;