rs10198628

Variant names:

• chr2-12824371-A-G
• rs10198628
• ENST00000663507.1:n.433-37391T>C

Your query was ambiguous. Multiple possible variants found:

• chr2-12824371-A-G
• chr2-12824371-A-T

Variant summary

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

The ENST00000663507.1(ENSG00000225649):​n.433-37391T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.588 in 151,936 control chromosomes in the GnomAD database, including 26,627 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 0.59 (26627 hom., cov: 31)
• Consequence: ENSG00000225649 ENST00000663507.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.00
• Publications: 21 publications found

Genes affected

ENSG00000225649 (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 (EAS) allele frequency at 95% confidence interval = 0.821 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000225649	ENST00000663507.1	n.433-37391T>C		intron_variant	Intron 4 of 6
ENSG00000225649	ENST00000848763.1	n.320-37391T>C		intron_variant	Intron 3 of 4
ENSG00000225649	ENST00000848764.1	n.325-86849T>C		intron_variant	Intron 2 of 3
ENSG00000225649	ENST00000848765.1	n.167-86849T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.588 AC: 89193 AN: 151818 Hom.: 26588 Cov.: 31

Gnomad AFR AF: 0.621

Gnomad AMI AF: 0.545

Gnomad AMR AF: 0.517

Gnomad ASJ AF: 0.579

Gnomad EAS AF: 0.841

Gnomad SAS AF: 0.628

Gnomad FIN AF: 0.658

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.552

Gnomad OTH AF: 0.567

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

GnomAD4 genome AF: 0.588 AC: 89286 AN: 151936 Hom.: 26627 Cov.: 31 AF XY: 0.589 AC XY: 43740 AN XY: 74236

African (AFR) AF: 0.622 AC: 25753 AN: 41428

American (AMR) AF: 0.517 AC: 7890 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.579 AC: 2009 AN: 3468

East Asian (EAS) AF: 0.841 AC: 4340 AN: 5158

South Asian (SAS) AF: 0.629 AC: 3029 AN: 4816

European-Finnish (FIN) AF: 0.658 AC: 6935 AN: 10540

Middle Eastern (MID) AF: 0.517 AC: 152 AN: 294

European-Non Finnish (NFE) AF: 0.552 AC: 37475 AN: 67942

Other (OTH) AF: 0.572 AC: 1206 AN: 2108

Alfa AF: 0.567 Hom.: 63533

Bravo AF: 0.579

Asia WGS AF: 0.713 AC: 2480 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	8.7
DANN	Benign	0.67
PhyloP100		1.0

Splicing

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

Other links and lift over

dbSNP: rs10198628; hg19: chr2-12964497;