rs10497464

Variant names:

• chr2-177071787-T-C
• rs10497464
• ENST00000441205.1:n.370+22788A>G

Variant summary

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

The ENST00000653899.1(ENSG00000229337):​n.607+22788A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0386 in 152,240 control chromosomes in the GnomAD database, including 289 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 0.039 (289 hom., cov: 32)
• Consequence: ENSG00000229337 ENST00000653899.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.883
• Publications: 4 publications found

Genes affected

ENSG00000229337 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.152 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000653899.1. 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
	ENSG00000229337	ENST00000441205.1	TSL:5	n.370+22788A>G		intron	N/A
	ENSG00000229337	ENST00000653899.1		n.607+22788A>G		intron	N/A
	ENSG00000229337	ENST00000657989.1		n.254+22788A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0386 AC: 5878 AN: 152122 Hom.: 286 Cov.: 32

Gnomad AFR AF: 0.0302

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.156

Gnomad ASJ AF: 0.0527

Gnomad EAS AF: 0.0882

Gnomad SAS AF: 0.0462

Gnomad FIN AF: 0.0378

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0126

Gnomad OTH AF: 0.0474

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

GnomAD4 genome AF: 0.0386 AC: 5884 AN: 152240 Hom.: 289 Cov.: 32 AF XY: 0.0432 AC XY: 3213 AN XY: 74440

African (AFR) AF: 0.0302 AC: 1254 AN: 41536

American (AMR) AF: 0.157 AC: 2395 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0527 AC: 183 AN: 3472

East Asian (EAS) AF: 0.0876 AC: 454 AN: 5180

South Asian (SAS) AF: 0.0458 AC: 221 AN: 4828

European-Finnish (FIN) AF: 0.0378 AC: 401 AN: 10606

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0126 AC: 859 AN: 68020

Other (OTH) AF: 0.0473 AC: 100 AN: 2112

Alfa AF: 0.0224 Hom.: 239

Bravo AF: 0.0462

Asia WGS AF: 0.0660 AC: 230 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	9.7
DANN	Benign	0.74
PhyloP100		0.88
Mutation Taster		=100/0	polymorphism

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: rs10497464;

hg19: chr2-177936515;