rs10195263

Variant names:

• chr2-150869278-G-A
• rs10195263
• ENST00000812494.1:n.382+45694C>T

Your query was ambiguous. Multiple possible variants found:

• chr2-150869278-G-A
• chr2-150869278-G-C

Variant summary

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

The ENST00000812494.1(ENSG00000222031):​n.382+45694C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.973 in 152,282 control chromosomes in the GnomAD database, including 72,101 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 0.97 (72101 hom., cov: 31)
• Consequence: ENSG00000222031 ENST00000812494.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13
• Publications: 10 publications found

Genes affected

ENSG00000222031 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.971 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000812494.1. 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
	ENSG00000222031	ENST00000812494.1		n.382+45694C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.973 AC: 148047 AN: 152164 Hom.: 72045 Cov.: 31

Gnomad AFR AF: 0.970

Gnomad AMI AF: 0.954

Gnomad AMR AF: 0.980

Gnomad ASJ AF: 0.989

Gnomad EAS AF: 0.892

Gnomad SAS AF: 0.956

Gnomad FIN AF: 0.988

Gnomad MID AF: 0.997

Gnomad NFE AF: 0.977

Gnomad OTH AF: 0.973

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

GnomAD4 genome AF: 0.973 AC: 148162 AN: 152282 Hom.: 72101 Cov.: 31 AF XY: 0.973 AC XY: 72447 AN XY: 74450

African (AFR) AF: 0.970 AC: 40303 AN: 41558

American (AMR) AF: 0.981 AC: 15002 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.989 AC: 3432 AN: 3470

East Asian (EAS) AF: 0.892 AC: 4603 AN: 5160

South Asian (SAS) AF: 0.957 AC: 4610 AN: 4818

European-Finnish (FIN) AF: 0.988 AC: 10496 AN: 10620

Middle Eastern (MID) AF: 0.997 AC: 293 AN: 294

European-Non Finnish (NFE) AF: 0.977 AC: 66500 AN: 68040

Other (OTH) AF: 0.973 AC: 2053 AN: 2110

Alfa AF: 0.974 Hom.: 282909

Bravo AF: 0.972

Asia WGS AF: 0.919 AC: 3198 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.70
DANN	Benign	0.45
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs10195263; hg19: chr2-151725792;