rs2079103

Variant names:

• chr5-132528814-A-C
• rs2079103
• ENST00000640655.2:c.-168-30470A>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000640655.2(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 ENST00000640655.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.904

Genes affected

ENSG00000283782 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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	ENST00000640655.2	c.-168-30470A>C		intron_variant	Intron 2 of 25	5		ENSP00000491596.2

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

Gnomad4 AFR AF: 0.398

Gnomad4 AMR AF: 0.725

Gnomad4 ASJ AF: 0.668

Gnomad4 EAS AF: 0.620

Gnomad4 SAS AF: 0.741

Gnomad4 FIN AF: 0.732

Gnomad4 NFE AF: 0.752

Gnomad4 OTH AF: 0.686

Alfa AF: 0.742 Hom.: 82772

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2079103; hg19: chr5-131864506;