rs10205982

Positions:

• chr2-48945289-G-A
• chr2-48945289-G-C

Variant summary

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

The ENST00000634588.1(ENSG00000282890):​n.303-927G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0436 in 152,274 control chromosomes in the GnomAD database, including 227 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 0.044 (227 hom., cov: 32)
• Consequence: ENST00000634588.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0608 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000634588.1	n.303-927G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.0437 AC: 6643 AN: 152156 Hom.: 227 Cov.: 32

Gnomad AFR AF: 0.0116

Gnomad AMI AF: 0.147

Gnomad AMR AF: 0.0472

Gnomad ASJ AF: 0.0718

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0147

Gnomad FIN AF: 0.0611

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0623

Gnomad OTH AF: 0.0464

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

GnomAD4 genome AF: 0.0436 AC: 6641 AN: 152274 Hom.: 227 Cov.: 32 AF XY: 0.0433 AC XY: 3227 AN XY: 74450

Gnomad4 AFR AF: 0.0116

Gnomad4 AMR AF: 0.0471

Gnomad4 ASJ AF: 0.0718

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0145

Gnomad4 FIN AF: 0.0611

Gnomad4 NFE AF: 0.0623

Gnomad4 OTH AF: 0.0459

Alfa AF: 0.0552 Hom.: 377

Bravo AF: 0.0418

Asia WGS AF: 0.00693 AC: 24 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.0060
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10205982; hg19: chr2-49172428;