11-2173580-T-C

Variant names:

• chr11-2173580-T-C
• rs7119275
• ENST00000729705.1:n.321-405T>C

Variant summary

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

The ENST00000729705.1(ENSG00000295384):​n.321-405T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.691 in 152,008 control chromosomes in the GnomAD database, including 36,672 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 0.69 (36672 hom., cov: 32)
• Consequence: ENSG00000295384 ENST00000729705.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.08
• Publications: 12 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=-0.91).
• 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: ENST00000729705.1. 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
	ENSG00000295384	ENST00000729705.1		n.321-405T>C		intron	N/A
	ENSG00000295395	ENST00000729780.1		n.396+1121A>G		intron	N/A
	ENSG00000295395	ENST00000729781.1		n.420+1121A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.691 AC: 104912 AN: 151890 Hom.: 36650 Cov.: 32

Gnomad AFR AF: 0.765

Gnomad AMI AF: 0.605

Gnomad AMR AF: 0.708

Gnomad ASJ AF: 0.636

Gnomad EAS AF: 0.915

Gnomad SAS AF: 0.817

Gnomad FIN AF: 0.668

Gnomad MID AF: 0.797

Gnomad NFE AF: 0.622

Gnomad OTH AF: 0.715

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

GnomAD4 genome AF: 0.691 AC: 104984 AN: 152008 Hom.: 36672 Cov.: 32 AF XY: 0.696 AC XY: 51691 AN XY: 74302

African (AFR) AF: 0.765 AC: 31694 AN: 41442

American (AMR) AF: 0.707 AC: 10804 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.636 AC: 2206 AN: 3470

East Asian (EAS) AF: 0.916 AC: 4721 AN: 5156

South Asian (SAS) AF: 0.817 AC: 3938 AN: 4822

European-Finnish (FIN) AF: 0.668 AC: 7057 AN: 10572

Middle Eastern (MID) AF: 0.816 AC: 240 AN: 294

European-Non Finnish (NFE) AF: 0.622 AC: 42258 AN: 67952

Other (OTH) AF: 0.718 AC: 1514 AN: 2110

Alfa AF: 0.659 Hom.: 4281

Bravo AF: 0.696

Asia WGS AF: 0.858 AC: 2986 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.9
DANN	Benign	0.81
PhyloP100		-3.1

Splicing

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

Other links and lift over

dbSNP: rs7119275; hg19: chr11-2194810;