chr11-114833570-T-C

Variant names:

• chr11-114833570-T-C
• rs10502195
• ENST00000751459.1:n.192+39111A>G

Variant summary

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

The ENST00000751459.1(ENSG00000297869):​n.192+39111A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.34 in 151,932 control chromosomes in the GnomAD database, including 9,131 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 0.34 (9131 hom., cov: 32)
• Consequence: ENSG00000297869 ENST00000751459.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0370
• Publications: 1 publications found

Genes affected

ENSG00000297869 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.556 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000751459.1. 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
	ENSG00000297869	ENST00000751459.1		n.192+39111A>G		intron	N/A
	ENSG00000297869	ENST00000751460.1		n.214+39111A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.341 AC: 51702 AN: 151814 Hom.: 9123 Cov.: 32

Gnomad AFR AF: 0.342

Gnomad AMI AF: 0.332

Gnomad AMR AF: 0.406

Gnomad ASJ AF: 0.332

Gnomad EAS AF: 0.572

Gnomad SAS AF: 0.417

Gnomad FIN AF: 0.304

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.309

Gnomad OTH AF: 0.315

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

GnomAD4 genome AF: 0.340 AC: 51732 AN: 151932 Hom.: 9131 Cov.: 32 AF XY: 0.347 AC XY: 25787 AN XY: 74256

African (AFR) AF: 0.342 AC: 14149 AN: 41402

American (AMR) AF: 0.406 AC: 6203 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.332 AC: 1154 AN: 3472

East Asian (EAS) AF: 0.573 AC: 2948 AN: 5146

South Asian (SAS) AF: 0.417 AC: 2007 AN: 4818

European-Finnish (FIN) AF: 0.304 AC: 3208 AN: 10564

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.309 AC: 20994 AN: 67942

Other (OTH) AF: 0.320 AC: 674 AN: 2108

Alfa AF: 0.322 Hom.: 1637

Bravo AF: 0.343

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	5.0
DANN	Benign	0.85
PhyloP100		-0.037

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: rs10502195;

hg19: chr11-114704292;