2-76267835-T-C

Variant names:

• chr2-76267835-T-C
• rs1526651
• ENST00000654219.1:n.84-73718T>C

Variant summary

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

The ENST00000654219.1(ENSG00000287172):​n.84-73718T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.957 in 151,600 control chromosomes in the GnomAD database, including 69,445 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 0.96 (69445 hom., cov: 27)
• Consequence: ENSG00000287172 ENST00000654219.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.168
• Publications: 0 publications found

Genes affected

ENSG00000287172 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.969 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287172	ENST00000654219.1	n.84-73718T>C		intron_variant	Intron 1 of 4
ENSG00000287172	ENST00000668214.1	n.56-73718T>C		intron_variant	Intron 1 of 3
ENSG00000287172	ENST00000669228.1	n.84-73718T>C		intron_variant	Intron 1 of 4
ENSG00000309755	ENST00000843691.1	n.348-7011A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.957 AC: 144967 AN: 151484 Hom.: 69402 Cov.: 27

Gnomad AFR AF: 0.935

Gnomad AMI AF: 0.944

Gnomad AMR AF: 0.979

Gnomad ASJ AF: 0.984

Gnomad EAS AF: 0.992

Gnomad SAS AF: 0.978

Gnomad FIN AF: 0.935

Gnomad MID AF: 0.991

Gnomad NFE AF: 0.963

Gnomad OTH AF: 0.967

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

GnomAD4 genome AF: 0.957 AC: 145068 AN: 151600 Hom.: 69445 Cov.: 27 AF XY: 0.957 AC XY: 70844 AN XY: 74040

African (AFR) AF: 0.935 AC: 38631 AN: 41336

American (AMR) AF: 0.979 AC: 14893 AN: 15212

Ashkenazi Jewish (ASJ) AF: 0.984 AC: 3412 AN: 3468

East Asian (EAS) AF: 0.992 AC: 5060 AN: 5100

South Asian (SAS) AF: 0.978 AC: 4705 AN: 4812

European-Finnish (FIN) AF: 0.935 AC: 9762 AN: 10444

Middle Eastern (MID) AF: 0.990 AC: 291 AN: 294

European-Non Finnish (NFE) AF: 0.963 AC: 65413 AN: 67914

Other (OTH) AF: 0.968 AC: 2040 AN: 2108

Alfa AF: 0.961 Hom.: 10326

Bravo AF: 0.960

Asia WGS AF: 0.978 AC: 3401 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.4
DANN	Benign	0.44
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs1526651; hg19: chr2-76494961;