rs1373692

Positions:

• chr5-40431081-A-C
• chr5-40431081-A-T

Variant summary

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

The ENST00000637776.1(ENSG00000283286):​n.1212A>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.589 in 152,010 control chromosomes in the GnomAD database, including 27,275 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 (27275 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: ENST00000637776.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.325

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.672 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
	ENST00000637776.1	n.1212A>C		non_coding_transcript_exon_variant	2/2	5

Frequencies

GnomAD3 genomes AF: 0.589 AC: 89476 AN: 151896 Hom.: 27262 Cov.: 32

Gnomad AFR AF: 0.679

Gnomad AMI AF: 0.598

Gnomad AMR AF: 0.487

Gnomad ASJ AF: 0.619

Gnomad EAS AF: 0.138

Gnomad SAS AF: 0.469

Gnomad FIN AF: 0.542

Gnomad MID AF: 0.671

Gnomad NFE AF: 0.605

Gnomad OTH AF: 0.593

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.589 AC: 89533 AN: 152010 Hom.: 27275 Cov.: 32 AF XY: 0.580 AC XY: 43125 AN XY: 74302

Gnomad4 AFR AF: 0.679

Gnomad4 AMR AF: 0.486

Gnomad4 ASJ AF: 0.619

Gnomad4 EAS AF: 0.138

Gnomad4 SAS AF: 0.468

Gnomad4 FIN AF: 0.542

Gnomad4 NFE AF: 0.605

Gnomad4 OTH AF: 0.595

Alfa AF: 0.586 Hom.: 55608

Bravo AF: 0.586

Asia WGS AF: 0.372 AC: 1293 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.7
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1373692; hg19: chr5-40431183;