2-71731350-C-T

Variant names:

• chr2-71731350-C-T
• rs2900976
• ENST00000793602.1:n.263+34456C>T

Variant summary

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

The ENST00000793602.1(ENSG00000303319):​n.263+34456C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.285 in 152,108 control chromosomes in the GnomAD database, including 6,652 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 0.28 (6652 hom., cov: 32)
• Consequence: ENSG00000303319 ENST00000793602.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.17
• Publications: 14 publications found

Genes affected

ENSG00000303319 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.49).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.34 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124907827	XR_007086966.1	n.838-11354C>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000303319	ENST00000793602.1	n.263+34456C>T		intron_variant	Intron 3 of 3
ENSG00000303319	ENST00000793603.1	n.141+13953C>T		intron_variant	Intron 1 of 1
ENSG00000303319	ENST00000793604.1	n.193-11354C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.285 AC: 43320 AN: 151990 Hom.: 6654 Cov.: 32

Gnomad AFR AF: 0.204

Gnomad AMI AF: 0.510

Gnomad AMR AF: 0.224

Gnomad ASJ AF: 0.261

Gnomad EAS AF: 0.101

Gnomad SAS AF: 0.291

Gnomad FIN AF: 0.396

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.344

Gnomad OTH AF: 0.256

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

GnomAD4 genome AF: 0.285 AC: 43341 AN: 152108 Hom.: 6652 Cov.: 32 AF XY: 0.284 AC XY: 21129 AN XY: 74330

African (AFR) AF: 0.204 AC: 8484 AN: 41500

American (AMR) AF: 0.223 AC: 3415 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.261 AC: 905 AN: 3472

East Asian (EAS) AF: 0.100 AC: 517 AN: 5152

South Asian (SAS) AF: 0.290 AC: 1399 AN: 4822

European-Finnish (FIN) AF: 0.396 AC: 4187 AN: 10582

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.344 AC: 23367 AN: 67970

Other (OTH) AF: 0.256 AC: 540 AN: 2110

Alfa AF: 0.308 Hom.: 23806

Bravo AF: 0.270

Asia WGS AF: 0.218 AC: 758 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.49
CADD	Benign	20
DANN	Benign	0.60
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs2900976; hg19: chr2-71958480;