5-102523613-C-T

Variant names:

• chr5-102523613-C-T
• rs1502844
• ENST00000797988.1:n.340-4827G>A

Variant summary

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

The ENST00000797988.1(ENSG00000303908):​n.340-4827G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.654 in 151,960 control chromosomes in the GnomAD database, including 32,754 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 0.65 (32754 hom., cov: 32)
• Consequence: ENSG00000303908 ENST00000797988.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.537
• Publications: 26 publications found

Genes affected

ENSG00000303908 (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 (AFR) allele frequency at 95% confidence interval = 0.684 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000303908	ENST00000797988.1	n.340-4827G>A		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.654 AC: 99367 AN: 151842 Hom.: 32722 Cov.: 32

Gnomad AFR AF: 0.690

Gnomad AMI AF: 0.689

Gnomad AMR AF: 0.579

Gnomad ASJ AF: 0.706

Gnomad EAS AF: 0.454

Gnomad SAS AF: 0.596

Gnomad FIN AF: 0.735

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.654

Gnomad OTH AF: 0.641

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

GnomAD4 genome AF: 0.654 AC: 99442 AN: 151960 Hom.: 32754 Cov.: 32 AF XY: 0.656 AC XY: 48719 AN XY: 74266

African (AFR) AF: 0.690 AC: 28625 AN: 41456

American (AMR) AF: 0.579 AC: 8831 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.706 AC: 2450 AN: 3472

East Asian (EAS) AF: 0.454 AC: 2343 AN: 5162

South Asian (SAS) AF: 0.596 AC: 2869 AN: 4814

European-Finnish (FIN) AF: 0.735 AC: 7776 AN: 10582

Middle Eastern (MID) AF: 0.585 AC: 172 AN: 294

European-Non Finnish (NFE) AF: 0.654 AC: 44406 AN: 67910

Other (OTH) AF: 0.636 AC: 1343 AN: 2110

Alfa AF: 0.650 Hom.: 66590

Bravo AF: 0.649

Asia WGS AF: 0.527 AC: 1829 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	3.1
DANN	Benign	0.32
PhyloP100		0.54

Splicing

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

Other links and lift over

dbSNP: rs1502844; hg19: chr5-101859317; COSMIC: COSV60174690;