rs968432

Variant names:

• chr20-4761636-A-C
• rs968432
• ENST00000617466.1:n.337A>C

Your query was ambiguous. Multiple possible variants found:

• chr20-4761636-A-C
• chr20-4761636-A-G
• chr20-4761636-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: ENSG00000278595 ENST00000617466.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.60

Genes affected

ENSG00000278595 (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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000278595	ENST00000617466.1	n.337A>C		non_coding_transcript_exon_variant	Exon 1 of 1	6

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;