11-2163618-G-T

Variant names:

• chr11-2163618-G-T
• rs3842727
• ENST00000729705.1:n.175-4193G>T

Variant summary

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

The ENST00000729705.1(ENSG00000295384):​n.175-4193G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.592 in 152,186 control chromosomes in the GnomAD database, including 30,172 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 0.59 (30172 hom., cov: 35)
• Consequence: ENSG00000295384 ENST00000729705.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.510
• Publications: 27 publications found

Genes affected

ENSG00000295384 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.933 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000295384	ENST00000729705.1	n.175-4193G>T		intron_variant	Intron 1 of 2
ENSG00000295384	ENST00000729706.1	n.226-4193G>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.592 AC: 90074 AN: 152068 Hom.: 30165 Cov.: 35

Gnomad AFR AF: 0.256

Gnomad AMI AF: 0.655

Gnomad AMR AF: 0.709

Gnomad ASJ AF: 0.697

Gnomad EAS AF: 0.955

Gnomad SAS AF: 0.824

Gnomad FIN AF: 0.740

Gnomad MID AF: 0.774

Gnomad NFE AF: 0.695

Gnomad OTH AF: 0.647

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

GnomAD4 genome AF: 0.592 AC: 90092 AN: 152186 Hom.: 30172 Cov.: 35 AF XY: 0.605 AC XY: 45014 AN XY: 74404

African (AFR) AF: 0.255 AC: 10613 AN: 41566

American (AMR) AF: 0.710 AC: 10861 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.697 AC: 2418 AN: 3470

East Asian (EAS) AF: 0.955 AC: 4931 AN: 5164

South Asian (SAS) AF: 0.824 AC: 3975 AN: 4826

European-Finnish (FIN) AF: 0.740 AC: 7856 AN: 10612

Middle Eastern (MID) AF: 0.777 AC: 227 AN: 292

European-Non Finnish (NFE) AF: 0.695 AC: 47246 AN: 67944

Other (OTH) AF: 0.652 AC: 1372 AN: 2104

Alfa AF: 0.625 Hom.: 11179

Bravo AF: 0.572

Asia WGS AF: 0.842 AC: 2929 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.8
DANN	Benign	0.94
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs3842727; hg19: chr11-2184848;