rs4697843

Variant names:

• chr4-11094134-G-A
• rs4697843
• ENST00000754158.1:n.195+8736G>A

Variant summary

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

The ENST00000754158.1(ENSG00000298262):​n.195+8736G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.507 in 151,920 control chromosomes in the GnomAD database, including 23,055 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 0.51 (23055 hom., cov: 33)
• Consequence: ENSG00000298262 ENST00000754158.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0900
• Publications: 0 publications found

Genes affected

ENSG00000298262 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.803 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
ENSG00000298262	ENST00000754158.1	n.195+8736G>A		intron_variant	Intron 2 of 5
ENSG00000298262	ENST00000754159.1	n.495-26630G>A		intron_variant	Intron 1 of 3
ENSG00000298262	ENST00000754160.1	n.486+27191G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.507 AC: 76911 AN: 151802 Hom.: 22995 Cov.: 33

Gnomad AFR AF: 0.810

Gnomad AMI AF: 0.387

Gnomad AMR AF: 0.489

Gnomad ASJ AF: 0.373

Gnomad EAS AF: 0.797

Gnomad SAS AF: 0.470

Gnomad FIN AF: 0.461

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.324

Gnomad OTH AF: 0.483

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

GnomAD4 genome AF: 0.507 AC: 77027 AN: 151920 Hom.: 23055 Cov.: 33 AF XY: 0.515 AC XY: 38253 AN XY: 74238

African (AFR) AF: 0.810 AC: 33605 AN: 41472

American (AMR) AF: 0.490 AC: 7469 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.373 AC: 1293 AN: 3468

East Asian (EAS) AF: 0.798 AC: 4127 AN: 5174

South Asian (SAS) AF: 0.468 AC: 2254 AN: 4818

European-Finnish (FIN) AF: 0.461 AC: 4830 AN: 10486

Middle Eastern (MID) AF: 0.333 AC: 98 AN: 294

European-Non Finnish (NFE) AF: 0.323 AC: 21976 AN: 67940

Other (OTH) AF: 0.486 AC: 1023 AN: 2104

Alfa AF: 0.450 Hom.: 2322

Bravo AF: 0.525

Asia WGS AF: 0.626 AC: 2156 AN: 3446

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.87
DANN	Benign	0.28
PhyloP100		-0.090

Splicing

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

Other links and lift over

dbSNP: rs4697843; hg19: chr4-11095758;