rs10497551

Variant names:

• chr2-179916817-C-T
• rs10497551
• ENST00000807586.1:n.241-536C>T

Variant summary

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

The ENST00000807586.1(ENSG00000304992):​n.241-536C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.146 in 152,060 control chromosomes in the GnomAD database, including 2,041 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 0.15 (2041 hom., cov: 32)
• Consequence: ENSG00000304992 ENST00000807586.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.25
• Publications: 2 publications found

Genes affected

ENSG00000304992 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.283 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000807586.1. 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
	ENSG00000304992	ENST00000807586.1		n.241-536C>T		intron	N/A
	ENSG00000304992	ENST00000807587.1		n.172-536C>T		intron	N/A
	ENSG00000304992	ENST00000807588.1		n.228-536C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.146 AC: 22203 AN: 151942 Hom.: 2032 Cov.: 32

Gnomad AFR AF: 0.136

Gnomad AMI AF: 0.0318

Gnomad AMR AF: 0.289

Gnomad ASJ AF: 0.0872

Gnomad EAS AF: 0.206

Gnomad SAS AF: 0.150

Gnomad FIN AF: 0.210

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.111

Gnomad OTH AF: 0.128

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

GnomAD4 genome AF: 0.146 AC: 22227 AN: 152060 Hom.: 2041 Cov.: 32 AF XY: 0.154 AC XY: 11448 AN XY: 74326

African (AFR) AF: 0.136 AC: 5645 AN: 41474

American (AMR) AF: 0.290 AC: 4428 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0872 AC: 302 AN: 3464

East Asian (EAS) AF: 0.206 AC: 1063 AN: 5160

South Asian (SAS) AF: 0.150 AC: 725 AN: 4824

European-Finnish (FIN) AF: 0.210 AC: 2215 AN: 10566

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.111 AC: 7523 AN: 67976

Other (OTH) AF: 0.128 AC: 270 AN: 2116

Alfa AF: 0.141 Hom.: 215

Bravo AF: 0.152

Asia WGS AF: 0.197 AC: 683 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.46
DANN	Benign	0.49
PhyloP100		-1.2

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: rs10497551;

hg19: chr2-180781544;