5-82927814-A-C

Variant names:

• chr5-82927814-A-C
• rs37554
• ENST00000504916.2:n.417-3467T>G

Variant summary

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

The ENST00000504916.2(ENSG00000248112):​n.417-3467T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.739 in 152,000 control chromosomes in the GnomAD database, including 43,503 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 0.74 (43503 hom., cov: 32)
• Consequence: ENSG00000248112 ENST00000504916.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.566
• Publications: 0 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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.84 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105379051	NR_188290.1	n.374-6701T>G		intron_variant	Intron 1 of 2
LOC105379051	NR_188291.1	n.374-6701T>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000248112	ENST00000504916.2	n.417-3467T>G		intron_variant	Intron 1 of 3	3
ENSG00000248112	ENST00000718043.1	n.554-6701T>G		intron_variant	Intron 2 of 3
ENSG00000248112	ENST00000718044.1	n.408-6701T>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.740 AC: 112359 AN: 151882 Hom.: 43503 Cov.: 32

Gnomad AFR AF: 0.491

Gnomad AMI AF: 0.865

Gnomad AMR AF: 0.789

Gnomad ASJ AF: 0.731

Gnomad EAS AF: 0.747

Gnomad SAS AF: 0.728

Gnomad FIN AF: 0.947

Gnomad MID AF: 0.715

Gnomad NFE AF: 0.846

Gnomad OTH AF: 0.748

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

GnomAD4 genome AF: 0.739 AC: 112395 AN: 152000 Hom.: 43503 Cov.: 32 AF XY: 0.744 AC XY: 55301 AN XY: 74282

African (AFR) AF: 0.491 AC: 20319 AN: 41382

American (AMR) AF: 0.789 AC: 12058 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.731 AC: 2537 AN: 3472

East Asian (EAS) AF: 0.746 AC: 3843 AN: 5150

South Asian (SAS) AF: 0.728 AC: 3501 AN: 4808

European-Finnish (FIN) AF: 0.947 AC: 10027 AN: 10592

Middle Eastern (MID) AF: 0.721 AC: 212 AN: 294

European-Non Finnish (NFE) AF: 0.846 AC: 57534 AN: 68002

Other (OTH) AF: 0.747 AC: 1577 AN: 2112

Alfa AF: 0.802 Hom.: 49305

Bravo AF: 0.715

Asia WGS AF: 0.708 AC: 2461 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	11
DANN	Benign	0.81
PhyloP100		0.57

Splicing

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

Other links and lift over

dbSNP: rs37554; hg19: chr5-82223633;