rs1713511

Variant names:

• chr4-43775353-G-A
• rs1713511
• ENST00000655512.1:n.117-3175G>A

Your query was ambiguous. Multiple possible variants found:

• chr4-43775353-G-A
• chr4-43775353-G-C
• chr4-43775353-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000655512.1(ENSG00000286891):​n.117-3175G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.274 in 150,008 control chromosomes in the GnomAD database, including 5,764 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 0.27 (5764 hom., cov: 28)
• Consequence: ENSG00000286891 ENST00000655512.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.73

Genes affected

ENSG00000286891 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.322 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
ENSG00000286891	ENST00000655512.1	n.117-3175G>A		intron_variant	Intron 1 of 4
ENSG00000286891	ENST00000665455.1	n.286+11578G>A		intron_variant	Intron 1 of 2
ENSG00000286891	ENST00000667550.1	n.310-3175G>A		intron_variant	Intron 1 of 3
ENSG00000286891	ENST00000669927.1	n.282-3175G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.274 AC: 41079 AN: 149892 Hom.: 5757 Cov.: 28

Gnomad AFR AF: 0.327

Gnomad AMI AF: 0.184

Gnomad AMR AF: 0.296

Gnomad ASJ AF: 0.219

Gnomad EAS AF: 0.121

Gnomad SAS AF: 0.191

Gnomad FIN AF: 0.208

Gnomad MID AF: 0.156

Gnomad NFE AF: 0.270

Gnomad OTH AF: 0.249

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

GnomAD4 genome AF: 0.274 AC: 41096 AN: 150008 Hom.: 5764 Cov.: 28 AF XY: 0.269 AC XY: 19685 AN XY: 73094

Gnomad4 AFR AF: 0.326

Gnomad4 AMR AF: 0.296

Gnomad4 ASJ AF: 0.219

Gnomad4 EAS AF: 0.122

Gnomad4 SAS AF: 0.190

Gnomad4 FIN AF: 0.208

Gnomad4 NFE AF: 0.270

Gnomad4 OTH AF: 0.246

Alfa AF: 0.265 Hom.: 6683

Bravo AF: 0.281

Asia WGS AF: 0.144 AC: 501 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.71
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1713511; hg19: chr4-43777370;