11-44055677-G-A

Position:

• chr11-44055677-G-A

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ACCSL	NM_001031854.2	c.1140-363G>A		intron_variant		ENST00000378832.1	NP_001027025.2
ACCSL	NM_001363113.1	c.597-363G>A		intron_variant			NP_001350042.1
ACCSL	XM_047426927.1	c.1188-363G>A		intron_variant			XP_047282883.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ACCSL	ENST00000378832.1	c.1140-363G>A		intron_variant		1	NM_001031854.2	ENSP00000368109	P1
ACCSL	ENST00000527145.1	c.*659-363G>A		intron_variant, NMD_transcript_variant		1		ENSP00000436505

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

Gnomad4 AFR AF: 0.0862

Gnomad4 AMR AF: 0.0871

Gnomad4 ASJ AF: 0.129

Gnomad4 EAS AF: 0.0640

Gnomad4 SAS AF: 0.0450

Gnomad4 FIN AF: 0.171

Gnomad4 NFE AF: 0.112

Gnomad4 OTH AF: 0.108

Alfa AF: 0.106 Hom.: 1216

Bravo AF: 0.0966

Asia WGS AF: 0.0460 AC: 159 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	9.5
DANN	Benign	0.69

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

Publications

LitVar

Other links and lift over

dbSNP: rs12284962; hg19: chr11-44077227;