chr2-74712049-T-C

Variant names:

• chr2-74712049-T-C
• rs1137
• ENST00000744271.1:n.97+3769A>G

Variant summary

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

The ENST00000744271.1(ENSG00000297014):​n.97+3769A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.595 in 152,146 control chromosomes in the GnomAD database, including 32,467 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 0.59 (32467 hom., cov: 31)
• Consequence: ENSG00000297014 ENST00000744271.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.899
• Publications: 15 publications found

Genes affected

ENSG00000297014 (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 (NFE) allele frequency at 95% confidence interval = 0.79 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
ENSG00000297014	ENST00000744271.1	n.97+3769A>G		intron_variant	Intron 1 of 1
ENSG00000297014	ENST00000744272.1	n.77+3769A>G		intron_variant	Intron 1 of 2
ENSG00000297014	ENST00000744273.1	n.90+3769A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.595 AC: 90512 AN: 152028 Hom.: 32469 Cov.: 31

Gnomad AFR AF: 0.202

Gnomad AMI AF: 0.706

Gnomad AMR AF: 0.684

Gnomad ASJ AF: 0.836

Gnomad EAS AF: 0.176

Gnomad SAS AF: 0.646

Gnomad FIN AF: 0.791

Gnomad MID AF: 0.769

Gnomad NFE AF: 0.796

Gnomad OTH AF: 0.668

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

GnomAD4 genome AF: 0.595 AC: 90524 AN: 152146 Hom.: 32467 Cov.: 31 AF XY: 0.595 AC XY: 44231 AN XY: 74380

African (AFR) AF: 0.201 AC: 8358 AN: 41486

American (AMR) AF: 0.684 AC: 10465 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.836 AC: 2902 AN: 3472

East Asian (EAS) AF: 0.176 AC: 910 AN: 5176

South Asian (SAS) AF: 0.645 AC: 3110 AN: 4818

European-Finnish (FIN) AF: 0.791 AC: 8379 AN: 10588

Middle Eastern (MID) AF: 0.769 AC: 226 AN: 294

European-Non Finnish (NFE) AF: 0.796 AC: 54121 AN: 68002

Other (OTH) AF: 0.669 AC: 1412 AN: 2112

Alfa AF: 0.730 Hom.: 129694

Bravo AF: 0.567

Asia WGS AF: 0.417 AC: 1451 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	0.60
DANN	Benign	0.54
PhyloP100		-0.90

Splicing

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

Other links and lift over

dbSNP: rs1137; hg19: chr2-74939176;