rs4952931

Positions:

• chr2-48944698-G-A
• chr2-48944698-G-C

Variant summary

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

The ENST00000634588.1(ENSG00000282890):​n.303-1518G>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 0.585 in 150,052 control chromosomes in the GnomAD database, including 25,651 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 0.59 (25651 hom., cov: 27)
• Consequence: ENST00000634588.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.256

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.695 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000634588.1	n.303-1518G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.585 AC: 87720 AN: 149946 Hom.: 25617 Cov.: 27

Gnomad AFR AF: 0.612

Gnomad AMI AF: 0.377

Gnomad AMR AF: 0.623

Gnomad ASJ AF: 0.514

Gnomad EAS AF: 0.714

Gnomad SAS AF: 0.640

Gnomad FIN AF: 0.627

Gnomad MID AF: 0.542

Gnomad NFE AF: 0.547

Gnomad OTH AF: 0.577

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

GnomAD4 genome AF: 0.585 AC: 87796 AN: 150052 Hom.: 25651 Cov.: 27 AF XY: 0.590 AC XY: 43161 AN XY: 73096

Gnomad4 AFR AF: 0.613

Gnomad4 AMR AF: 0.623

Gnomad4 ASJ AF: 0.514

Gnomad4 EAS AF: 0.714

Gnomad4 SAS AF: 0.640

Gnomad4 FIN AF: 0.627

Gnomad4 NFE AF: 0.547

Gnomad4 OTH AF: 0.573

Alfa AF: 0.554 Hom.: 29302

Bravo AF: 0.583

Asia WGS AF: 0.666 AC: 2308 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.76
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4952931; hg19: chr2-49171837;