11-35068797-A-G

Variant names:

• chr11-35068797-A-G
• rs675970
• ENST00000747995.1:n.136+5958A>G

Variant summary

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

The ENST00000747995.1(ENSG00000297460):​n.136+5958A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.666 in 152,122 control chromosomes in the GnomAD database, including 34,849 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 0.67 (34849 hom., cov: 33)
• Consequence: ENSG00000297460 ENST00000747995.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.608
• Publications: 8 publications found

Genes affected

ENSG00000297460 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.825 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000747995.1. 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
	ENSG00000297460	ENST00000747995.1		n.136+5958A>G		intron	N/A
	ENSG00000297460	ENST00000747996.1		n.84+18672A>G		intron	N/A
	ENSG00000297460	ENST00000747997.1		n.83+18672A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.666 AC: 101284 AN: 152004 Hom.: 34799 Cov.: 33

Gnomad AFR AF: 0.832

Gnomad AMI AF: 0.570

Gnomad AMR AF: 0.668

Gnomad ASJ AF: 0.643

Gnomad EAS AF: 0.790

Gnomad SAS AF: 0.781

Gnomad FIN AF: 0.545

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.568

Gnomad OTH AF: 0.678

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

GnomAD4 genome AF: 0.666 AC: 101387 AN: 152122 Hom.: 34849 Cov.: 33 AF XY: 0.669 AC XY: 49776 AN XY: 74360

African (AFR) AF: 0.832 AC: 34546 AN: 41506

American (AMR) AF: 0.668 AC: 10221 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.643 AC: 2229 AN: 3468

East Asian (EAS) AF: 0.789 AC: 4091 AN: 5182

South Asian (SAS) AF: 0.780 AC: 3763 AN: 4824

European-Finnish (FIN) AF: 0.545 AC: 5748 AN: 10552

Middle Eastern (MID) AF: 0.724 AC: 213 AN: 294

European-Non Finnish (NFE) AF: 0.568 AC: 38621 AN: 67986

Other (OTH) AF: 0.680 AC: 1437 AN: 2112

Alfa AF: 0.541 Hom.: 2311

Bravo AF: 0.679

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.3
DANN	Benign	0.78
PhyloP100		-0.61

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: rs675970;

hg19: chr11-35090344;