5-40799438-G-A

Variant names:

• chr5-40799438-G-A
• rs461404
• ENST00000691528.3:n.1198G>A

Variant summary

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

The ENST00000691528.3(ENSG00000288911):​n.1198G>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 0.705 in 152,114 control chromosomes in the GnomAD database, including 37,793 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 0.70 (37793 hom., cov: 34)
• Consequence: ENSG00000288911 ENST00000691528.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.134
• Publications: 13 publications found

Genes affected

ENSG00000288911 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.782 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000691528.3. 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
	ENSG00000288911	ENST00000691528.3		n.1198G>A		non_coding_transcript_exon	Exon 1 of 1

Frequencies

GnomAD3 genomes AF: 0.705 AC: 107119 AN: 151996 Hom.: 37759 Cov.: 34

Gnomad AFR AF: 0.683

Gnomad AMI AF: 0.697

Gnomad AMR AF: 0.760

Gnomad ASJ AF: 0.658

Gnomad EAS AF: 0.802

Gnomad SAS AF: 0.708

Gnomad FIN AF: 0.691

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.704

Gnomad OTH AF: 0.681

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

GnomAD4 genome AF: 0.705 AC: 107208 AN: 152114 Hom.: 37793 Cov.: 34 AF XY: 0.707 AC XY: 52619 AN XY: 74380

African (AFR) AF: 0.683 AC: 28344 AN: 41484

American (AMR) AF: 0.760 AC: 11615 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.658 AC: 2282 AN: 3468

East Asian (EAS) AF: 0.802 AC: 4156 AN: 5182

South Asian (SAS) AF: 0.710 AC: 3422 AN: 4818

European-Finnish (FIN) AF: 0.691 AC: 7313 AN: 10578

Middle Eastern (MID) AF: 0.619 AC: 182 AN: 294

European-Non Finnish (NFE) AF: 0.704 AC: 47836 AN: 67988

Other (OTH) AF: 0.674 AC: 1424 AN: 2112

Alfa AF: 0.703 Hom.: 20809

Bravo AF: 0.707

Asia WGS AF: 0.709 AC: 2466 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.4
DANN	Benign	0.41
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs461404; hg19: chr5-40799540;