5-40407216-G-A

Variant names:

• chr5-40407216-G-A
• rs16869977
• ENST00000800852.1:n.537-64G>A

Variant summary

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

The ENST00000800852.1(ENSG00000304179):​n.537-64G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0858 in 152,202 control chromosomes in the GnomAD database, including 790 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 0.086 (790 hom., cov: 32)
• Consequence: ENSG00000304179 ENST00000800852.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0680
• Publications: 8 publications found

Genes affected

ENSG00000304179 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.188 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000800852.1. 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
	ENSG00000304179	ENST00000800852.1		n.537-64G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0857 AC: 13030 AN: 152084 Hom.: 781 Cov.: 32

Gnomad AFR AF: 0.0485

Gnomad AMI AF: 0.0691

Gnomad AMR AF: 0.193

Gnomad ASJ AF: 0.0901

Gnomad EAS AF: 0.118

Gnomad SAS AF: 0.0590

Gnomad FIN AF: 0.0448

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0900

Gnomad OTH AF: 0.0894

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

GnomAD4 genome AF: 0.0858 AC: 13063 AN: 152202 Hom.: 790 Cov.: 32 AF XY: 0.0856 AC XY: 6372 AN XY: 74408

African (AFR) AF: 0.0486 AC: 2021 AN: 41550

American (AMR) AF: 0.194 AC: 2961 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.0901 AC: 313 AN: 3472

East Asian (EAS) AF: 0.118 AC: 607 AN: 5154

South Asian (SAS) AF: 0.0597 AC: 288 AN: 4824

European-Finnish (FIN) AF: 0.0448 AC: 476 AN: 10614

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.0901 AC: 6124 AN: 68002

Other (OTH) AF: 0.0894 AC: 189 AN: 2114

Alfa AF: 0.0872 Hom.: 333

Bravo AF: 0.0995

Asia WGS AF: 0.0690 AC: 240 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	6.6
DANN	Benign	0.68
PhyloP100		-0.068

Splicing

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

Other links and lift over

dbSNP: rs16869977; hg19: chr5-40407318;