ENST00000617466.1:n.337A>C

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

Genes affected

ENSG00000278595 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000617466.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000278595	ENST00000617466.1	TSL:6	n.337A>C		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000278595	ENST00000758402.1		n.993A>C		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000278595	ENST00000758403.1		n.1046A>C		non_coding_transcript_exon	Exon 2 of 2

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.875 AC: 7 AN: 8

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.806 AC: 33433 AN: 41490

American (AMR) AF: 0.963 AC: 14743 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.980 AC: 3404 AN: 3472

East Asian (EAS) AF: 0.996 AC: 5162 AN: 5182

South Asian (SAS) AF: 0.956 AC: 4605 AN: 4818

European-Finnish (FIN) AF: 0.958 AC: 10158 AN: 10608

Middle Eastern (MID) AF: 0.966 AC: 284 AN: 294

European-Non Finnish (NFE) AF: 0.957 AC: 65075 AN: 68034

Other (OTH) AF: 0.935 AC: 1974 AN: 2112

Alfa AF: 0.932 Hom.: 16185

Bravo AF: 0.914

Asia WGS AF: 0.963 AC: 3348 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.5
DANN	Benign	0.82
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs968432; hg19: chr20-4742282;