rs7578654

Positions:

• chr2-49283034-A-C
• chr2-49283034-A-G

Variant summary

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

The ENST00000634588.1(ENSG00000282890):​n.493-125168A>C 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 0.427 in 494,086 control chromosomes in the GnomAD database, including 45,741 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 0.45 (15268 hom., cov: 33)
  • Exomes 𝑓: 0.42 (30473 hom.)
• Consequence: ENST00000634588.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.394

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.482 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.493-125168A>C		intron_variant, non_coding_transcript_variant		5
	ENST00000635306.1	n.407+48840T>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.448 AC: 67935 AN: 151536 Hom.: 15245 Cov.: 33

Gnomad AFR AF: 0.487

Gnomad AMI AF: 0.426

Gnomad AMR AF: 0.389

Gnomad ASJ AF: 0.407

Gnomad EAS AF: 0.391

Gnomad SAS AF: 0.425

Gnomad FIN AF: 0.440

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.448

Gnomad OTH AF: 0.437

GnomAD3 exomes AF: 0.419 AC: 91900 AN: 219402 Hom.: 19609 AF XY: 0.419 AC XY: 50990 AN XY: 121820

Gnomad AFR exome AF: 0.481

Gnomad AMR exome AF: 0.381

Gnomad ASJ exome AF: 0.396

Gnomad EAS exome AF: 0.376

Gnomad SAS exome AF: 0.404

Gnomad FIN exome AF: 0.424

Gnomad NFE exome AF: 0.437

Gnomad OTH exome AF: 0.401

GnomAD4 exome AF: 0.417 AC: 142816 AN: 342432 Hom.: 30473 Cov.: 0 AF XY: 0.417 AC XY: 82541 AN XY: 197834

Gnomad4 AFR exome AF: 0.477

Gnomad4 AMR exome AF: 0.378

Gnomad4 ASJ exome AF: 0.393

Gnomad4 EAS exome AF: 0.369

Gnomad4 SAS exome AF: 0.403

Gnomad4 FIN exome AF: 0.421

Gnomad4 NFE exome AF: 0.432

Gnomad4 OTH exome AF: 0.412

GnomAD4 genome AF: 0.448 AC: 68010 AN: 151654 Hom.: 15268 Cov.: 33 AF XY: 0.447 AC XY: 33095 AN XY: 74102

Gnomad4 AFR AF: 0.488

Gnomad4 AMR AF: 0.390

Gnomad4 ASJ AF: 0.407

Gnomad4 EAS AF: 0.391

Gnomad4 SAS AF: 0.425

Gnomad4 FIN AF: 0.440

Gnomad4 NFE AF: 0.448

Gnomad4 OTH AF: 0.436

Alfa AF: 0.438 Hom.: 31182

Bravo AF: 0.446

Asia WGS AF: 0.424 AC: 1475 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	9.3
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7578654; hg19: chr2-49510173;