rs1373692

Variant names:

• chr5-40431081-A-C
• rs1373692
• ENST00000637776.1:n.1212A>C

Your query was ambiguous. Multiple possible variants found:

• chr5-40431081-A-C
• chr5-40431081-A-G
• 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: ENSG00000283286 ENST00000637776.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.325

Genes affected

ENSG00000283286 (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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000283286	ENST00000637776.1	n.1212A>C		non_coding_transcript_exon_variant	Exon 2 of 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;