11-72809485-C-G

Variant names:

• chr11-72809485-C-G
• rs4944804
• ENST00000719214.1:n.441C>G

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_Strong BS2

The ENST00000719214.1(ENSG00000293817):​n.441C>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00905 in 152,212 control chromosomes in the GnomAD database, including 11 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 0.0090 (11 hom., cov: 31)
• Consequence: ENSG00000293817 ENST00000719214.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.410
• Publications: 20 publications found

Genes affected

ENSG00000293817 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BS2: High Homozygotes in GnomAd4 at 11 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000719214.1. 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
	ENSG00000293817	ENST00000719214.1		n.441C>G		non_coding_transcript_exon	Exon 3 of 4
	ENSG00000293817	ENST00000719215.1		n.556C>G		non_coding_transcript_exon	Exon 3 of 4
	ENSG00000293817	ENST00000719218.1		n.293C>G		non_coding_transcript_exon	Exon 3 of 4

Frequencies

GnomAD3 genomes AF: 0.00905 AC: 1377 AN: 152094 Hom.: 11 Cov.: 31

Gnomad AFR AF: 0.00217

Gnomad AMI AF: 0.0396

Gnomad AMR AF: 0.00707

Gnomad ASJ AF: 0.0109

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.00145

Gnomad FIN AF: 0.0210

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0127

Gnomad OTH AF: 0.00478

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

GnomAD4 genome AF: 0.00905 AC: 1377 AN: 152212 Hom.: 11 Cov.: 31 AF XY: 0.00912 AC XY: 679 AN XY: 74430

African (AFR) AF: 0.00217 AC: 90 AN: 41540

American (AMR) AF: 0.00706 AC: 108 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0109 AC: 38 AN: 3472

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5186

South Asian (SAS) AF: 0.00145 AC: 7 AN: 4822

European-Finnish (FIN) AF: 0.0210 AC: 223 AN: 10594

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.0127 AC: 862 AN: 67992

Other (OTH) AF: 0.00473 AC: 10 AN: 2114

Alfa AF: 0.000197 Hom.: 10370

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	4.5
DANN	Benign	0.85
PhyloP100		0.41

Splicing

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

Other links and lift over

dbSNP: rs4944804; hg19: chr11-72520530;