11-44055677-G-A

Variant names:

• chr11-44055677-G-A
• rs12284962
• NM_001031854.2:c.1140-363G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001031854.2(ACCSL):​c.1140-363G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.103 in 152,270 control chromosomes in the GnomAD database, including 934 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 0.10 (934 hom., cov: 33)
• Consequence: ACCSL NM_001031854.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.33
• Publications: 1 publications found

Genes affected

ACCSL (HGNC:34391): (1-aminocyclopropane-1-carboxylate synthase homolog (inactive) like) Predicted to enable catalytic activity and pyridoxal phosphate binding activity. Predicted to be involved in biosynthetic process. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.109 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001031854.2. 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
	ACCSL	NM_001031854.2	MANE Select	c.1140-363G>A		intron	N/A	NP_001027025.2
	ACCSL	NM_001363113.1		c.597-363G>A		intron	N/A	NP_001350042.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ACCSL	ENST00000378832.1	TSL:1 MANE Select	c.1140-363G>A		intron	N/A	ENSP00000368109.1
	ACCSL	ENST00000527145.1	TSL:1	n.*659-363G>A		intron	N/A	ENSP00000436505.1

Frequencies

GnomAD3 genomes AF: 0.103 AC: 15643 AN: 152152 Hom.: 927 Cov.: 33

Gnomad AFR AF: 0.0856

Gnomad AMI AF: 0.120

Gnomad AMR AF: 0.0872

Gnomad ASJ AF: 0.129

Gnomad EAS AF: 0.0640

Gnomad SAS AF: 0.0456

Gnomad FIN AF: 0.171

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.112

Gnomad OTH AF: 0.107

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.103 AC: 15677 AN: 152270 Hom.: 934 Cov.: 33 AF XY: 0.104 AC XY: 7751 AN XY: 74454

African (AFR) AF: 0.0862 AC: 3583 AN: 41564

American (AMR) AF: 0.0871 AC: 1332 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.129 AC: 447 AN: 3470

East Asian (EAS) AF: 0.0640 AC: 332 AN: 5190

South Asian (SAS) AF: 0.0450 AC: 217 AN: 4820

European-Finnish (FIN) AF: 0.171 AC: 1812 AN: 10606

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.112 AC: 7589 AN: 68014

Other (OTH) AF: 0.108 AC: 228 AN: 2112

Alfa AF: 0.106 Hom.: 2641

Bravo AF: 0.0966

Asia WGS AF: 0.0460 AC: 159 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	9.5
DANN	Benign	0.69
PhyloP100		1.3
Mutation Taster		=100/0	polymorphism (auto)

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: rs12284962; hg19: chr11-44077227;