rs11735008

Variant names:

• chr4-409514-A-G
• rs11735008
• ENST00000631198.1:n.138+23203A>G

Variant summary

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

The ENST00000631198.1(ENSG00000281016):​n.138+23203A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.255 in 152,068 control chromosomes in the GnomAD database, including 5,017 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 0.25 (5017 hom., cov: 32)
• Consequence: ENSG00000281016 ENST00000631198.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.703
• Publications: 1 publications found

Genes affected

ENSG00000281016 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.27 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000631198.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000281016	ENST00000631198.1	TSL:3	n.138+23203A>G		intron	N/A
	ENSG00000281016	ENST00000816209.1		n.184-9257A>G		intron	N/A
	ENSG00000281016	ENST00000816210.1		n.169-9257A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.255 AC: 38707 AN: 151950 Hom.: 5017 Cov.: 32

Gnomad AFR AF: 0.211

Gnomad AMI AF: 0.263

Gnomad AMR AF: 0.234

Gnomad ASJ AF: 0.305

Gnomad EAS AF: 0.179

Gnomad SAS AF: 0.238

Gnomad FIN AF: 0.355

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.273

Gnomad OTH AF: 0.275

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

GnomAD4 genome AF: 0.255 AC: 38721 AN: 152068 Hom.: 5017 Cov.: 32 AF XY: 0.258 AC XY: 19140 AN XY: 74328

African (AFR) AF: 0.211 AC: 8776 AN: 41500

American (AMR) AF: 0.234 AC: 3568 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.305 AC: 1059 AN: 3472

East Asian (EAS) AF: 0.179 AC: 928 AN: 5174

South Asian (SAS) AF: 0.237 AC: 1144 AN: 4826

European-Finnish (FIN) AF: 0.355 AC: 3749 AN: 10548

Middle Eastern (MID) AF: 0.367 AC: 108 AN: 294

European-Non Finnish (NFE) AF: 0.273 AC: 18569 AN: 67956

Other (OTH) AF: 0.275 AC: 581 AN: 2112

Alfa AF: 0.264 Hom.: 688

Bravo AF: 0.246

Asia WGS AF: 0.224 AC: 780 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	5.7
DANN	Benign	0.43
PhyloP100		-0.70

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs11735008;

hg19: chr4-403303;