rs1349311

Variant names:

• chr3-3602762-G-A
• rs1349311
• ENST00000420000.6:n.200+23982C>T

Your query was ambiguous. Multiple possible variants found:

• chr3-3602762-G-A
• chr3-3602762-G-T

Variant summary

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

The ENST00000420000.6(ENSG00000223727):​n.200+23982C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.765 in 152,020 control chromosomes in the GnomAD database, including 45,557 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 0.77 (45557 hom., cov: 31)
• Consequence: ENSG00000223727 ENST00000420000.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.368
• Publications: 1 publications found

Genes affected

ENSG00000223727 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.841 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
ENSG00000223727	ENST00000420000.6	n.200+23982C>T		intron_variant	Intron 2 of 4	4

Frequencies

GnomAD3 genomes AF: 0.765 AC: 116237 AN: 151902 Hom.: 45530 Cov.: 31

Gnomad AFR AF: 0.587

Gnomad AMI AF: 0.909

Gnomad AMR AF: 0.769

Gnomad ASJ AF: 0.754

Gnomad EAS AF: 0.751

Gnomad SAS AF: 0.830

Gnomad FIN AF: 0.893

Gnomad MID AF: 0.813

Gnomad NFE AF: 0.847

Gnomad OTH AF: 0.778

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

GnomAD4 genome AF: 0.765 AC: 116305 AN: 152020 Hom.: 45557 Cov.: 31 AF XY: 0.768 AC XY: 57075 AN XY: 74294

African (AFR) AF: 0.587 AC: 24320 AN: 41432

American (AMR) AF: 0.769 AC: 11745 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.754 AC: 2616 AN: 3468

East Asian (EAS) AF: 0.751 AC: 3854 AN: 5134

South Asian (SAS) AF: 0.830 AC: 4003 AN: 4820

European-Finnish (FIN) AF: 0.893 AC: 9470 AN: 10604

Middle Eastern (MID) AF: 0.816 AC: 240 AN: 294

European-Non Finnish (NFE) AF: 0.847 AC: 57587 AN: 67986

Other (OTH) AF: 0.780 AC: 1643 AN: 2106

Alfa AF: 0.788 Hom.: 5955

Bravo AF: 0.745

Asia WGS AF: 0.786 AC: 2729 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.93
DANN	Benign	0.48
PhyloP100		-0.37

Splicing

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

Other links and lift over

dbSNP: rs1349311; hg19: chr3-3644446;