chr5-82938978-G-A

Variant names:

• chr5-82938978-G-A
• rs37545
• ENST00000504916.2:n.417-14631C>T

Variant summary

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

The ENST00000504916.2(ENSG00000248112):​n.417-14631C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.561 in 151,940 control chromosomes in the GnomAD database, including 24,688 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 0.56 (24688 hom., cov: 32)
• Consequence: ENSG00000248112 ENST00000504916.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.492
• Publications: 3 publications found

Genes affected

ENSG00000248112 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.619 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105379051	NR_188290.1	n.374-17865C>T		intron_variant	Intron 1 of 2
LOC105379051	NR_188291.1	n.374-17865C>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000248112	ENST00000504916.2	n.417-14631C>T		intron_variant	Intron 1 of 3	3
ENSG00000248112	ENST00000718043.1	n.554-17865C>T		intron_variant	Intron 2 of 3
ENSG00000248112	ENST00000718044.1	n.408-17865C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.561 AC: 85221 AN: 151820 Hom.: 24691 Cov.: 32

Gnomad AFR AF: 0.422

Gnomad AMI AF: 0.467

Gnomad AMR AF: 0.558

Gnomad ASJ AF: 0.484

Gnomad EAS AF: 0.625

Gnomad SAS AF: 0.475

Gnomad FIN AF: 0.756

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.624

Gnomad OTH AF: 0.532

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

GnomAD4 genome AF: 0.561 AC: 85240 AN: 151940 Hom.: 24688 Cov.: 32 AF XY: 0.565 AC XY: 41963 AN XY: 74308

African (AFR) AF: 0.422 AC: 17484 AN: 41412

American (AMR) AF: 0.559 AC: 8515 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.484 AC: 1677 AN: 3466

East Asian (EAS) AF: 0.625 AC: 3222 AN: 5158

South Asian (SAS) AF: 0.474 AC: 2286 AN: 4818

European-Finnish (FIN) AF: 0.756 AC: 7995 AN: 10576

Middle Eastern (MID) AF: 0.439 AC: 129 AN: 294

European-Non Finnish (NFE) AF: 0.624 AC: 42400 AN: 67954

Other (OTH) AF: 0.525 AC: 1109 AN: 2112

Alfa AF: 0.588 Hom.: 85969

Bravo AF: 0.538

Asia WGS AF: 0.501 AC: 1746 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.51
DANN	Benign	0.42
PhyloP100		-0.49

Splicing

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

Other links and lift over

dbSNP: rs37545; hg19: chr5-82234797;