rs2276695

Variant names:

• chr2-118057292-C-T
• rs2276695
• ENST00000747789.1:n.232-11599G>A

Variant summary

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

The ENST00000747789.1(ENSG00000297418):​n.232-11599G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.416 in 151,940 control chromosomes in the GnomAD database, including 13,621 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 0.42 (13621 hom., cov: 32)
• Consequence: ENSG00000297418 ENST00000747789.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0370
• Publications: 6 publications found

Genes affected

ENSG00000297418 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.524 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102723413	XR_427162.4	n.382-340C>T		intron_variant	Intron 4 of 4
LOC102723413	XR_923247.3	n.261-340C>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000297418	ENST00000747789.1	n.232-11599G>A		intron_variant	Intron 2 of 4
ENSG00000297418	ENST00000747790.1	n.105-26973G>A		intron_variant	Intron 1 of 2
ENSG00000297418	ENST00000747791.1	n.550+5506G>A		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.416 AC: 63202 AN: 151822 Hom.: 13613 Cov.: 32

Gnomad AFR AF: 0.530

Gnomad AMI AF: 0.424

Gnomad AMR AF: 0.406

Gnomad ASJ AF: 0.412

Gnomad EAS AF: 0.431

Gnomad SAS AF: 0.411

Gnomad FIN AF: 0.275

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.371

Gnomad OTH AF: 0.399

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

GnomAD4 genome AF: 0.416 AC: 63238 AN: 151940 Hom.: 13621 Cov.: 32 AF XY: 0.412 AC XY: 30593 AN XY: 74252

African (AFR) AF: 0.530 AC: 21954 AN: 41440

American (AMR) AF: 0.406 AC: 6199 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.412 AC: 1429 AN: 3470

East Asian (EAS) AF: 0.430 AC: 2214 AN: 5144

South Asian (SAS) AF: 0.410 AC: 1970 AN: 4800

European-Finnish (FIN) AF: 0.275 AC: 2899 AN: 10542

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.371 AC: 25232 AN: 67960

Other (OTH) AF: 0.393 AC: 831 AN: 2116

Alfa AF: 0.387 Hom.: 14241

Bravo AF: 0.432

Asia WGS AF: 0.395 AC: 1376 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	4.5
DANN	Benign	0.74
PhyloP100		-0.037

Splicing

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

Other links and lift over

dbSNP: rs2276695; hg19: chr2-118814868;