2-195007095-C-T

Variant names:

• chr2-195007095-C-T
• rs10172965
• ENST00000418387.1:n.147-2503G>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000418387.1(ENSG00000235056):​n.147-2503G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.287 in 151,130 control chromosomes in the GnomAD database, including 8,237 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 0.29 (8237 hom., cov: 32)
• Consequence: ENSG00000235056 ENST00000418387.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.319

Genes affected

ENSG00000235056 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.52).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.54 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376755	XR_007088699.1	n.265+52340G>A		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000235056	ENST00000418387.1	n.147-2503G>A		intron_variant	Intron 1 of 1	5

Frequencies

GnomAD3 genomes AF: 0.286 AC: 43259 AN: 151012 Hom.: 8196 Cov.: 32

Gnomad AFR AF: 0.545

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.164

Gnomad ASJ AF: 0.147

Gnomad EAS AF: 0.289

Gnomad SAS AF: 0.202

Gnomad FIN AF: 0.150

Gnomad MID AF: 0.172

Gnomad NFE AF: 0.194

Gnomad OTH AF: 0.247

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

GnomAD4 genome AF: 0.287 AC: 43350 AN: 151130 Hom.: 8237 Cov.: 32 AF XY: 0.281 AC XY: 20724 AN XY: 73826

Gnomad4 AFR AF: 0.546

Gnomad4 AMR AF: 0.164

Gnomad4 ASJ AF: 0.147

Gnomad4 EAS AF: 0.290

Gnomad4 SAS AF: 0.202

Gnomad4 FIN AF: 0.150

Gnomad4 NFE AF: 0.194

Gnomad4 OTH AF: 0.247

Alfa AF: 0.202 Hom.: 6523

Bravo AF: 0.302

Asia WGS AF: 0.297 AC: 1031 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.52
CADD	Benign	15
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10172965; hg19: chr2-195871819;