rs968432

chr20-4761636-A-Cchr20-4761636-A-Gchr20-4761636-A-T

Variant summary

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

The ENST00000617466.1(ENSG00000278595):n.337A>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 0.917 in 152,230 control chromosomes in the GnomAD database, including 64,440 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 0.92 (64437 hom., cov: 32)
  • Exomes 𝑓: 0.88 (3 hom.)
• Consequence: ENST00000617466.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.60

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.973 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
	ENST00000617466.1	n.337A>C		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.918 AC: 139564 AN: 152104 Hom.: 64394 Cov.: 32

Gnomad AFR AF: 0.806

Gnomad AMI AF: 0.905

Gnomad AMR AF: 0.963

Gnomad ASJ AF: 0.980

Gnomad EAS AF: 0.996

Gnomad SAS AF: 0.956

Gnomad FIN AF: 0.958

Gnomad MID AF: 0.962

Gnomad NFE AF: 0.956

Gnomad OTH AF: 0.934

GnomAD4 exome AF: 0.875 AC: 7 AN: 8 Hom.: 3 Cov.: 0 AC XY: 0 AN XY: 0

Gnomad4 FIN exome AF: 0.875

GnomAD4 genome AF: 0.917 AC: 139662 AN: 152222 Hom.: 64437 Cov.: 32 AF XY: 0.920 AC XY: 68446 AN XY: 74420

Gnomad4 AFR AF: 0.806

Gnomad4 AMR AF: 0.963

Gnomad4 ASJ AF: 0.980

Gnomad4 EAS AF: 0.996

Gnomad4 SAS AF: 0.956

Gnomad4 FIN AF: 0.958

Gnomad4 NFE AF: 0.957

Gnomad4 OTH AF: 0.935

Alfa AF: 0.935 Hom.: 15925

Bravo AF: 0.914

Asia WGS AF: 0.963 AC: 3348 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	1.5
Dann	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs968432; hg19: chr20-4742282;