rs11005115

Variant names:

• chr10-55927510-G-A
• rs11005115
• ENST00000837206.1:n.316+11140C>T

Variant summary

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

The ENST00000837206.1(ENSG00000308905):​n.316+11140C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.299 in 151,984 control chromosomes in the GnomAD database, including 8,341 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 0.30 (8341 hom., cov: 31)
• Consequence: ENSG00000308905 ENST00000837206.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.626
• Publications: 2 publications found

Genes affected

ENSG00000308905 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.521 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000837206.1. 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
	ENSG00000308905	ENST00000837206.1		n.316+11140C>T		intron	N/A
	ENSG00000308905	ENST00000837209.1		n.317-235C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.299 AC: 45415 AN: 151866 Hom.: 8351 Cov.: 31

Gnomad AFR AF: 0.0808

Gnomad AMI AF: 0.391

Gnomad AMR AF: 0.345

Gnomad ASJ AF: 0.400

Gnomad EAS AF: 0.539

Gnomad SAS AF: 0.328

Gnomad FIN AF: 0.333

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.388

Gnomad OTH AF: 0.333

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

GnomAD4 genome AF: 0.299 AC: 45392 AN: 151984 Hom.: 8341 Cov.: 31 AF XY: 0.299 AC XY: 22222 AN XY: 74246

African (AFR) AF: 0.0807 AC: 3345 AN: 41474

American (AMR) AF: 0.345 AC: 5265 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.400 AC: 1388 AN: 3466

East Asian (EAS) AF: 0.537 AC: 2769 AN: 5152

South Asian (SAS) AF: 0.327 AC: 1577 AN: 4822

European-Finnish (FIN) AF: 0.333 AC: 3508 AN: 10544

Middle Eastern (MID) AF: 0.425 AC: 125 AN: 294

European-Non Finnish (NFE) AF: 0.388 AC: 26363 AN: 67938

Other (OTH) AF: 0.329 AC: 696 AN: 2114

Alfa AF: 0.325 Hom.: 1625

Bravo AF: 0.291

Asia WGS AF: 0.371 AC: 1292 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.28
DANN	Benign	0.35
PhyloP100		-0.63

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: rs11005115;

hg19: chr10-57687270;