rs1952613917

Variant names:

• chr11-44048368-C-A
• rs1952613917
• NM_001031854.2:c.332C>A

Your query was ambiguous. Multiple possible variants found:

• chr11-44048368-C-A
• chr11-44048368-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001031854.2(ACCSL):​c.332C>A​(p.Ala111Asp) variant causes a missense 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. 16/21 in silico tools predict 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: 31)
• Consequence: ACCSL NM_001031854.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0480

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 Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.07959777).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ACCSL	NM_001031854.2	c.332C>A	p.Ala111Asp	missense_variant	Exon 1 of 14	ENST00000378832.1	NP_001027025.2
ACCSL	XM_047426927.1	c.380C>A	p.Ala127Asp	missense_variant	Exon 5 of 18		XP_047282883.1
ACCSL	NM_001363113.1	c.-259C>A		5_prime_UTR_variant	Exon 1 of 14		NP_001350042.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ACCSL	ENST00000378832.1	c.332C>A	p.Ala111Asp	missense_variant	Exon 1 of 14	1	NM_001031854.2	ENSP00000368109.1
ACCSL	ENST00000527145.1	n.332C>A		non_coding_transcript_exon_variant	Exon 1 of 14	1		ENSP00000436505.1

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.098
BayesDel_addAF	Benign	-0.12	T
BayesDel_noAF	Benign	-0.42
CADD	Benign	2.7
DANN	Benign	0.84
DEOGEN2	Benign	0.042	T
Eigen	Benign	-1.1
Eigen_PC	Benign	-1.2
FATHMM_MKL	Benign	0.028	N
LIST_S2	Benign	0.32	T
M_CAP	Benign	0.019	T
MetaRNN	Benign	0.080	T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	1.6	L
PrimateAI	Benign	0.26	T
PROVEAN	Benign	-1.2	N
REVEL	Benign	0.19
Sift	Benign	0.27	T
Sift4G	Benign	0.59	T
Polyphen		0.20	B
Vest4		0.14
MutPred		0.20		Loss of helix (P = 0.0068);
MVP		0.092
MPC		0.39
ClinPred		0.11	T
GERP RS		-0.53
Varity_R		0.069
gMVP		0.16

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: rs1952613917; hg19: chr11-44069918;