rs11735070

Variant names:

• chr4-99792608-G-C
• rs11735070
• ENST00000795494.1:n.175+29035C>G

Variant summary

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

The ENST00000795494.1(ENSG00000303547):​n.175+29035C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.331 in 151,948 control chromosomes in the GnomAD database, including 8,584 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 0.33 (8584 hom., cov: 31)
• Consequence: ENSG00000303547 ENST00000795494.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.33
• Publications: 9 publications found

Genes affected

ENSG00000303547 (HGNC:58858):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.379 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000795494.1. 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
	ENSG00000303547	ENST00000795494.1		n.175+29035C>G		intron	N/A
	ENSG00000303547	ENST00000795495.1		n.349+29035C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.331 AC: 50305 AN: 151832 Hom.: 8566 Cov.: 31

Gnomad AFR AF: 0.277

Gnomad AMI AF: 0.355

Gnomad AMR AF: 0.387

Gnomad ASJ AF: 0.400

Gnomad EAS AF: 0.392

Gnomad SAS AF: 0.206

Gnomad FIN AF: 0.264

Gnomad MID AF: 0.382

Gnomad NFE AF: 0.361

Gnomad OTH AF: 0.374

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

GnomAD4 genome AF: 0.331 AC: 50368 AN: 151948 Hom.: 8584 Cov.: 31 AF XY: 0.327 AC XY: 24291 AN XY: 74282

African (AFR) AF: 0.278 AC: 11506 AN: 41436

American (AMR) AF: 0.387 AC: 5912 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.400 AC: 1385 AN: 3464

East Asian (EAS) AF: 0.393 AC: 2032 AN: 5170

South Asian (SAS) AF: 0.206 AC: 994 AN: 4822

European-Finnish (FIN) AF: 0.264 AC: 2787 AN: 10540

Middle Eastern (MID) AF: 0.380 AC: 111 AN: 292

European-Non Finnish (NFE) AF: 0.361 AC: 24524 AN: 67934

Other (OTH) AF: 0.376 AC: 794 AN: 2114

Alfa AF: 0.338 Hom.: 1084

Bravo AF: 0.341

Asia WGS AF: 0.292 AC: 1016 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.17
DANN	Benign	0.45
PhyloP100		-1.3

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: rs11735070;

hg19: chr4-100713765;