rs3917368

Variant names:

• chr2-112825205-C-T
• rs3917368
• ENST00000762706.1:n.404+54309C>T

Variant summary

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

The ENST00000762706.1(ENSG00000299339):​n.404+54309C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.294 in 152,152 control chromosomes in the GnomAD database, including 7,232 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 0.29 (7232 hom., cov: 32)
• Consequence: ENSG00000299339 ENST00000762706.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.31
• Publications: 27 publications found

Genes affected

ENSG00000299339 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.504 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
ENSG00000299339	ENST00000762706.1	n.404+54309C>T		intron_variant	Intron 2 of 3
ENSG00000299339	ENST00000762707.1	n.499+54309C>T		intron_variant	Intron 2 of 2
ENSG00000299339	ENST00000762708.1	n.265+54309C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.294 AC: 44704 AN: 152032 Hom.: 7237 Cov.: 32

Gnomad AFR AF: 0.167

Gnomad AMI AF: 0.363

Gnomad AMR AF: 0.288

Gnomad ASJ AF: 0.333

Gnomad EAS AF: 0.520

Gnomad SAS AF: 0.251

Gnomad FIN AF: 0.268

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.359

Gnomad OTH AF: 0.314

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

GnomAD4 genome AF: 0.294 AC: 44700 AN: 152152 Hom.: 7232 Cov.: 32 AF XY: 0.291 AC XY: 21609 AN XY: 74374

African (AFR) AF: 0.166 AC: 6910 AN: 41528

American (AMR) AF: 0.288 AC: 4395 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.333 AC: 1154 AN: 3468

East Asian (EAS) AF: 0.521 AC: 2699 AN: 5182

South Asian (SAS) AF: 0.251 AC: 1211 AN: 4822

European-Finnish (FIN) AF: 0.268 AC: 2827 AN: 10566

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.359 AC: 24438 AN: 67990

Other (OTH) AF: 0.310 AC: 653 AN: 2108

Alfa AF: 0.341 Hom.: 15162

Bravo AF: 0.294

Asia WGS AF: 0.326 AC: 1134 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	7.5
DANN	Benign	0.70
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs3917368; hg19: chr2-113582782;