11-270715-T-C

Variant names:

• chr11-270715-T-C
• rs17655730
• ENST00000835501.1:n.275+9102A>G

Variant summary

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

The ENST00000835501.1(ENSG00000293500):​n.275+9102A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.192 in 152,040 control chromosomes in the GnomAD database, including 3,278 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 0.19 (3278 hom., cov: 32)
• Consequence: ENSG00000293500 ENST00000835501.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.94
• Publications: 32 publications found

Genes affected

ENSG00000293500 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.231 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000835501.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000293500	ENST00000835501.1		n.275+9102A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.192 AC: 29239 AN: 151922 Hom.: 3276 Cov.: 32

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.184

Gnomad AMR AF: 0.194

Gnomad ASJ AF: 0.101

Gnomad EAS AF: 0.00231

Gnomad SAS AF: 0.105

Gnomad FIN AF: 0.367

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.234

Gnomad OTH AF: 0.191

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

GnomAD4 genome AF: 0.192 AC: 29256 AN: 152040 Hom.: 3278 Cov.: 32 AF XY: 0.197 AC XY: 14651 AN XY: 74332

African (AFR) AF: 0.122 AC: 5054 AN: 41472

American (AMR) AF: 0.194 AC: 2969 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.101 AC: 351 AN: 3460

East Asian (EAS) AF: 0.00232 AC: 12 AN: 5174

South Asian (SAS) AF: 0.105 AC: 508 AN: 4818

European-Finnish (FIN) AF: 0.367 AC: 3879 AN: 10564

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.234 AC: 15895 AN: 67956

Other (OTH) AF: 0.189 AC: 399 AN: 2106

Alfa AF: 0.218 Hom.: 9395

Bravo AF: 0.180

Asia WGS AF: 0.0590 AC: 209 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.96
DANN	Benign	0.24
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs17655730; hg19: chr11-270715;