chr5-82912453-G-A

Variant names:

• chr5-82912453-G-A
• rs673871
• ENST00000718048.1:n.693-4411C>T

Variant summary

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

The ENST00000718048.1(ENSG00000248112):​n.693-4411C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0433 in 152,194 control chromosomes in the GnomAD database, including 291 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 0.043 (291 hom., cov: 32)
• Consequence: ENSG00000248112 ENST00000718048.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.38
• 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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.206 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107986430	XR_001742771.2	n.152+716G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000248112	ENST00000718048.1	n.693-4411C>T		intron_variant	Intron 3 of 4
ENSG00000248112	ENST00000718049.1	n.389-49293C>T		intron_variant	Intron 1 of 1
ENSG00000248112	ENST00000745102.1	n.233+8509C>T		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.0433 AC: 6590 AN: 152076 Hom.: 292 Cov.: 32

Gnomad AFR AF: 0.0121

Gnomad AMI AF: 0.0164

Gnomad AMR AF: 0.0410

Gnomad ASJ AF: 0.00749

Gnomad EAS AF: 0.218

Gnomad SAS AF: 0.0476

Gnomad FIN AF: 0.0968

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0434

Gnomad OTH AF: 0.0407

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

GnomAD4 genome AF: 0.0433 AC: 6592 AN: 152194 Hom.: 291 Cov.: 32 AF XY: 0.0465 AC XY: 3459 AN XY: 74400

African (AFR) AF: 0.0122 AC: 505 AN: 41528

American (AMR) AF: 0.0410 AC: 626 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.00749 AC: 26 AN: 3472

East Asian (EAS) AF: 0.217 AC: 1121 AN: 5166

South Asian (SAS) AF: 0.0477 AC: 230 AN: 4826

European-Finnish (FIN) AF: 0.0968 AC: 1023 AN: 10572

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.0435 AC: 2956 AN: 68030

Other (OTH) AF: 0.0417 AC: 88 AN: 2108

Alfa AF: 0.0448 Hom.: 27

Bravo AF: 0.0381

Asia WGS AF: 0.117 AC: 407 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.018
DANN	Benign	0.36
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs673871; hg19: chr5-82208272;