chr2-148630399-T-C

Variant names:

• chr2-148630399-T-C
• rs10191411
• ENST00000724408.1:n.89-12553T>C

Variant summary

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

The ENST00000724408.1(ENSG00000294568):​n.89-12553T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.558 in 152,108 control chromosomes in the GnomAD database, including 27,094 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 0.56 (27094 hom., cov: 33)
• Consequence: ENSG00000294568 ENST00000724408.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.32
• Publications: 13 publications found

Genes affected

ENSG00000294568 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.724 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000724408.1. 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
	ENSG00000294568	ENST00000724408.1		n.89-12553T>C		intron	N/A
	ENSG00000294568	ENST00000724409.1		n.286-12553T>C		intron	N/A
	ENSG00000294568	ENST00000724410.1		n.432+11012T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.559 AC: 84907 AN: 151990 Hom.: 27104 Cov.: 33

Gnomad AFR AF: 0.301

Gnomad AMI AF: 0.870

Gnomad AMR AF: 0.540

Gnomad ASJ AF: 0.677

Gnomad EAS AF: 0.121

Gnomad SAS AF: 0.463

Gnomad FIN AF: 0.685

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.730

Gnomad OTH AF: 0.563

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

GnomAD4 genome AF: 0.558 AC: 84893 AN: 152108 Hom.: 27094 Cov.: 33 AF XY: 0.552 AC XY: 41029 AN XY: 74372

African (AFR) AF: 0.300 AC: 12456 AN: 41484

American (AMR) AF: 0.539 AC: 8233 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.677 AC: 2350 AN: 3470

East Asian (EAS) AF: 0.121 AC: 630 AN: 5192

South Asian (SAS) AF: 0.463 AC: 2229 AN: 4816

European-Finnish (FIN) AF: 0.685 AC: 7247 AN: 10572

Middle Eastern (MID) AF: 0.578 AC: 170 AN: 294

European-Non Finnish (NFE) AF: 0.730 AC: 49612 AN: 67990

Other (OTH) AF: 0.557 AC: 1173 AN: 2106

Alfa AF: 0.658 Hom.: 121275

Bravo AF: 0.531

Asia WGS AF: 0.301 AC: 1051 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.0
DANN	Benign	0.78
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs10191411; hg19: chr2-149387968;