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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000793602.1. 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
	ENSG00000303319	ENST00000793602.1		n.263+34456C>T		intron	N/A
	ENSG00000303319	ENST00000793603.1		n.141+13953C>T		intron	N/A
	ENSG00000303319	ENST00000793604.1		n.193-11354C>T		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2900976;

hg19: chr2-71958480;