4-43775353-G-A

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

Genes affected

ENSG00000286891 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000655512.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000286891	ENST00000655512.1		n.117-3175G>A		intron	N/A
	ENSG00000286891	ENST00000665455.2		n.308+11578G>A		intron	N/A
	ENSG00000286891	ENST00000667550.1		n.310-3175G>A		intron	N/A

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

African (AFR) AF: 0.326 AC: 13315 AN: 40816

American (AMR) AF: 0.296 AC: 4430 AN: 14960

Ashkenazi Jewish (ASJ) AF: 0.219 AC: 759 AN: 3460

East Asian (EAS) AF: 0.122 AC: 613 AN: 5034

South Asian (SAS) AF: 0.190 AC: 902 AN: 4756

European-Finnish (FIN) AF: 0.208 AC: 2116 AN: 10184

Middle Eastern (MID) AF: 0.153 AC: 44 AN: 288

European-Non Finnish (NFE) AF: 0.270 AC: 18242 AN: 67536

Other (OTH) AF: 0.246 AC: 509 AN: 2072

Alfa AF: 0.268 Hom.: 8497

Bravo AF: 0.281

Asia WGS AF: 0.144 AC: 501 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.71
DANN	Benign	0.76
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs1713511; hg19: chr4-43777370;