5-40410482-T-C

Variant names:

• chr5-40410482-T-C
• rs11742570
• ENST00000809861.1:n.360A>G

Variant summary

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

The ENST00000809861.1(ENSG00000305258):​n.360A>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 0.571 in 151,972 control chromosomes in the GnomAD database, including 25,451 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 0.57 (25451 hom., cov: 31)
• Consequence: ENSG00000305258 ENST00000809861.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.49
• Publications: 74 publications found

Genes affected

ENSG00000305258 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.605 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000809861.1. 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
	ENSG00000305258	ENST00000809861.1		n.360A>G		non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.571 AC: 86643 AN: 151852 Hom.: 25436 Cov.: 31

Gnomad AFR AF: 0.612

Gnomad AMI AF: 0.728

Gnomad AMR AF: 0.475

Gnomad ASJ AF: 0.618

Gnomad EAS AF: 0.143

Gnomad SAS AF: 0.470

Gnomad FIN AF: 0.544

Gnomad MID AF: 0.662

Gnomad NFE AF: 0.606

Gnomad OTH AF: 0.578

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

GnomAD4 genome AF: 0.571 AC: 86703 AN: 151972 Hom.: 25451 Cov.: 31 AF XY: 0.563 AC XY: 41802 AN XY: 74260

African (AFR) AF: 0.612 AC: 25335 AN: 41426

American (AMR) AF: 0.474 AC: 7243 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.618 AC: 2144 AN: 3468

East Asian (EAS) AF: 0.143 AC: 739 AN: 5170

South Asian (SAS) AF: 0.470 AC: 2268 AN: 4828

European-Finnish (FIN) AF: 0.544 AC: 5730 AN: 10530

Middle Eastern (MID) AF: 0.644 AC: 188 AN: 292

European-Non Finnish (NFE) AF: 0.606 AC: 41164 AN: 67958

Other (OTH) AF: 0.581 AC: 1228 AN: 2114

Alfa AF: 0.588 Hom.: 97821

Bravo AF: 0.564

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	0.27
DANN	Benign	0.75
PhyloP100		-2.5

Splicing

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

Other links and lift over

dbSNP: rs11742570; hg19: chr5-40410584;