rs4944804

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr11-72809485-C-A
• chr11-72809485-C-G

Variant summary

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

The ENST00000719214.1(ENSG00000293817):​n.441C>A 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 0.205 in 152,182 control chromosomes in the GnomAD database, including 4,186 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 0.20 (4186 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.294 is higher than 0.05.

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>A		non_coding_transcript_exon	Exon 3 of 4
	ENSG00000293817	ENST00000719215.1		n.556C>A		non_coding_transcript_exon	Exon 3 of 4
	ENSG00000293817	ENST00000719218.1		n.293C>A		non_coding_transcript_exon	Exon 3 of 4

Frequencies

GnomAD3 genomes AF: 0.205 AC: 31149 AN: 152064 Hom.: 4183 Cov.: 31

Gnomad AFR AF: 0.0562

Gnomad AMI AF: 0.547

Gnomad AMR AF: 0.224

Gnomad ASJ AF: 0.248

Gnomad EAS AF: 0.0612

Gnomad SAS AF: 0.183

Gnomad FIN AF: 0.197

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.297

Gnomad OTH AF: 0.225

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

GnomAD4 genome AF: 0.205 AC: 31153 AN: 152182 Hom.: 4186 Cov.: 31 AF XY: 0.199 AC XY: 14794 AN XY: 74410

African (AFR) AF: 0.0561 AC: 2330 AN: 41532

American (AMR) AF: 0.224 AC: 3431 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.248 AC: 862 AN: 3472

East Asian (EAS) AF: 0.0613 AC: 318 AN: 5184

South Asian (SAS) AF: 0.184 AC: 885 AN: 4816

European-Finnish (FIN) AF: 0.197 AC: 2086 AN: 10592

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.297 AC: 20197 AN: 67984

Other (OTH) AF: 0.223 AC: 471 AN: 2114

Alfa AF: 0.250 Hom.: 10370

Bravo AF: 0.204

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	4.5
DANN	Benign	0.88
PhyloP100		0.41

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4944804;

hg19: chr11-72520530;