chr20-34922859-A-T

Variant names:

• chr20-34922859-A-T
• rs6087649
• NM_018677.4:c.1549-464A>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_018677.4(ACSS2):​c.1549-464A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ACSS2 NM_018677.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.334
• Publications: 7 publications found

Genes affected

ACSS2 (HGNC:15814): (acyl-CoA synthetase short chain family member 2) This gene encodes a cytosolic enzyme that catalyzes the activation of acetate for use in lipid synthesis and energy generation. The protein acts as a monomer and produces acetyl-CoA from acetate in a reaction that requires ATP. Expression of this gene is regulated by sterol regulatory element-binding proteins, transcription factors that activate genes required for the synthesis of cholesterol and unsaturated fatty acids. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2009]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018677.4. 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
	ACSS2	NM_018677.4	MANE Select	c.1549-464A>T		intron	N/A	NP_061147.1
	ACSS2	NM_001076552.3		c.1588-464A>T		intron	N/A	NP_001070020.2
	ACSS2	NM_001242393.2		c.1264-464A>T		intron	N/A	NP_001229322.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ACSS2	ENST00000360596.7	TSL:1 MANE Select	c.1549-464A>T		intron	N/A	ENSP00000353804.2
	ACSS2	ENST00000494727.1	TSL:2	n.18A>T		non_coding_transcript_exon	Exon 1 of 5
	ACSS2	ENST00000253382.5	TSL:2	c.1588-464A>T		intron	N/A	ENSP00000253382.5

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 5838 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 3150

African (AFR) AF: 0.00 AC: 0 AN: 92

American (AMR) AF: 0.00 AC: 0 AN: 1132

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 86

East Asian (EAS) AF: 0.00 AC: 0 AN: 582

South Asian (SAS) AF: 0.00 AC: 0 AN: 568

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 138

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 8

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 3010

Other (OTH) AF: 0.00 AC: 0 AN: 222

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	12
DANN	Benign	0.88
PhyloP100		0.33

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs6087649; hg19: chr20-33510662;