11-2174607-A-G

Variant names:

• chr11-2174607-A-G
• rs10840495
• ENST00000729780.1:n.396+94T>C

Variant summary

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

The ENST00000729780.1(ENSG00000295395):​n.396+94T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.661 in 151,632 control chromosomes in the GnomAD database, including 33,296 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 0.66 (33296 hom., cov: 33)
• Consequence: ENSG00000295395 ENST00000729780.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.99
• Publications: 10 publications found

Genes affected

ENSG00000295395 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.894 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000729780.1. 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
	ENSG00000295395	ENST00000729780.1		n.396+94T>C		intron	N/A
	ENSG00000295395	ENST00000729781.1		n.420+94T>C		intron	N/A
	ENSG00000295395	ENST00000729782.1		n.501+94T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.661 AC: 100140 AN: 151516 Hom.: 33290 Cov.: 33

Gnomad AFR AF: 0.665

Gnomad AMI AF: 0.602

Gnomad AMR AF: 0.692

Gnomad ASJ AF: 0.635

Gnomad EAS AF: 0.916

Gnomad SAS AF: 0.816

Gnomad FIN AF: 0.666

Gnomad MID AF: 0.785

Gnomad NFE AF: 0.621

Gnomad OTH AF: 0.694

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

GnomAD4 genome AF: 0.661 AC: 100182 AN: 151632 Hom.: 33296 Cov.: 33 AF XY: 0.667 AC XY: 49396 AN XY: 74092

African (AFR) AF: 0.664 AC: 27459 AN: 41346

American (AMR) AF: 0.692 AC: 10559 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.635 AC: 2202 AN: 3468

East Asian (EAS) AF: 0.916 AC: 4706 AN: 5138

South Asian (SAS) AF: 0.815 AC: 3924 AN: 4812

European-Finnish (FIN) AF: 0.666 AC: 6999 AN: 10514

Middle Eastern (MID) AF: 0.803 AC: 233 AN: 290

European-Non Finnish (NFE) AF: 0.621 AC: 42090 AN: 67798

Other (OTH) AF: 0.697 AC: 1466 AN: 2104

Alfa AF: 0.642 Hom.: 3905

Bravo AF: 0.662

Asia WGS AF: 0.850 AC: 2955 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.75
DANN	Benign	0.53
PhyloP100		-3.0

Splicing

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

Other links and lift over

dbSNP: rs10840495; hg19: chr11-2195837;