rs1343863

Variant names:

• chr4-180056827-G-A
• rs1343863
• ENST00000663768.1:n.503+714C>T

Your query was ambiguous. Multiple possible variants found:

• chr4-180056827-G-A
• chr4-180056827-G-C
• chr4-180056827-G-T

Variant summary

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

The ENST00000663768.1(ENSG00000287083):​n.503+714C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.571 in 152,086 control chromosomes in the GnomAD database, including 28,664 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 0.57 (28664 hom., cov: 32)
• Consequence: ENSG00000287083 ENST00000663768.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.539
• Publications: 8 publications found

Genes affected

ENSG00000287083 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.745 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
ENSG00000287083	ENST00000663768.1	n.503+714C>T		intron_variant	Intron 2 of 6
ENSG00000287083	ENST00000826563.1	n.146+2073C>T		intron_variant	Intron 1 of 6
ENSG00000287083	ENST00000826564.1	n.255+2726C>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.571 AC: 86820 AN: 151968 Hom.: 28662 Cov.: 32

Gnomad AFR AF: 0.240

Gnomad AMI AF: 0.860

Gnomad AMR AF: 0.503

Gnomad ASJ AF: 0.679

Gnomad EAS AF: 0.540

Gnomad SAS AF: 0.536

Gnomad FIN AF: 0.778

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.750

Gnomad OTH AF: 0.597

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

GnomAD4 genome AF: 0.571 AC: 86818 AN: 152086 Hom.: 28664 Cov.: 32 AF XY: 0.568 AC XY: 42234 AN XY: 74332

African (AFR) AF: 0.239 AC: 9933 AN: 41474

American (AMR) AF: 0.503 AC: 7674 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.679 AC: 2355 AN: 3470

East Asian (EAS) AF: 0.540 AC: 2782 AN: 5152

South Asian (SAS) AF: 0.535 AC: 2580 AN: 4822

European-Finnish (FIN) AF: 0.778 AC: 8235 AN: 10586

Middle Eastern (MID) AF: 0.636 AC: 187 AN: 294

European-Non Finnish (NFE) AF: 0.751 AC: 51038 AN: 68004

Other (OTH) AF: 0.592 AC: 1250 AN: 2110

Alfa AF: 0.643 Hom.: 19114

Bravo AF: 0.538

Asia WGS AF: 0.487 AC: 1695 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.098
DANN	Benign	0.60
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs1343863; hg19: chr4-180977980;