rs2079103

Variant names:

• chr5-132528814-A-C
• rs2079103
• ENST00000638452.2:c.-168-30470A>C

Variant summary

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

The ENST00000638452.2(ENSG00000283782):​c.-168-30470A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.644 in 152,194 control chromosomes in the GnomAD database, including 33,500 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 0.64 (33500 hom., cov: 34)
• Consequence: ENSG00000283782 ENST00000638452.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.904
• Publications: 14 publications found

Genes affected

ENSG00000283782 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.747 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
ENSG00000283782	ENST00000638452.2	c.-168-30470A>C		intron_variant	Intron 3 of 26	5		ENSP00000492349.2

Frequencies

GnomAD3 genomes AF: 0.644 AC: 97976 AN: 152074 Hom.: 33485 Cov.: 34

Gnomad AFR AF: 0.398

Gnomad AMI AF: 0.840

Gnomad AMR AF: 0.725

Gnomad ASJ AF: 0.668

Gnomad EAS AF: 0.620

Gnomad SAS AF: 0.742

Gnomad FIN AF: 0.732

Gnomad MID AF: 0.658

Gnomad NFE AF: 0.752

Gnomad OTH AF: 0.682

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

GnomAD4 genome AF: 0.644 AC: 98027 AN: 152194 Hom.: 33500 Cov.: 34 AF XY: 0.646 AC XY: 48034 AN XY: 74404

African (AFR) AF: 0.398 AC: 16514 AN: 41514

American (AMR) AF: 0.725 AC: 11100 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.668 AC: 2319 AN: 3470

East Asian (EAS) AF: 0.620 AC: 3208 AN: 5176

South Asian (SAS) AF: 0.741 AC: 3576 AN: 4824

European-Finnish (FIN) AF: 0.732 AC: 7750 AN: 10594

Middle Eastern (MID) AF: 0.653 AC: 192 AN: 294

European-Non Finnish (NFE) AF: 0.752 AC: 51156 AN: 68000

Other (OTH) AF: 0.686 AC: 1451 AN: 2116

Alfa AF: 0.717 Hom.: 131206

Bravo AF: 0.631

Asia WGS AF: 0.676 AC: 2352 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	4.8
DANN	Benign	0.44
PhyloP100		0.90

Splicing

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

Other links and lift over

dbSNP: rs2079103; hg19: chr5-131864506;