rs11024665

Variant names:

• chr11-18466672-G-A
• rs11024665
• NM_144972.5:c.418+862G>A

Your query was ambiguous. Multiple possible variants found:

• chr11-18466672-G-A
• chr11-18466672-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_144972.5(LDHAL6A):​c.418+862G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.114 in 133,822 control chromosomes in the GnomAD database, including 1,090 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 0.11 (1090 hom., cov: 28)
• Consequence: LDHAL6A NM_144972.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.68

Genes affected

LDHAL6A (HGNC:28335): (lactate dehydrogenase A like 6A) Predicted to enable L-lactate dehydrogenase activity. Predicted to be involved in carbohydrate metabolic process and carboxylic acid metabolic process. Located in extracellular exosome. [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=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.237 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LDHAL6A	NM_144972.5	c.418+862G>A		intron_variant	Intron 3 of 6	ENST00000280706.3	NP_659409.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LDHAL6A	ENST00000280706.3	c.418+862G>A		intron_variant	Intron 3 of 6	2	NM_144972.5	ENSP00000280706.2
LDHAL6A	ENST00000396213.7	c.418+862G>A		intron_variant	Intron 4 of 7	1		ENSP00000379516.3

Frequencies

GnomAD3 genomes AF: 0.114 AC: 15251 AN: 133802 Hom.: 1087 Cov.: 28

Gnomad AFR AF: 0.0427

Gnomad AMI AF: 0.0616

Gnomad AMR AF: 0.135

Gnomad ASJ AF: 0.126

Gnomad EAS AF: 0.227

Gnomad SAS AF: 0.250

Gnomad FIN AF: 0.204

Gnomad MID AF: 0.128

Gnomad NFE AF: 0.120

Gnomad OTH AF: 0.138

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

GnomAD4 genome AF: 0.114 AC: 15252 AN: 133822 Hom.: 1090 Cov.: 28 AF XY: 0.120 AC XY: 7703 AN XY: 64348

Gnomad4 AFR AF: 0.0427

Gnomad4 AMR AF: 0.135

Gnomad4 ASJ AF: 0.126

Gnomad4 EAS AF: 0.226

Gnomad4 SAS AF: 0.250

Gnomad4 FIN AF: 0.204

Gnomad4 NFE AF: 0.120

Gnomad4 OTH AF: 0.142

Alfa AF: 0.0956 Hom.: 321

Bravo AF: 0.105

Asia WGS AF: 0.199 AC: 615 AN: 3090

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.091
DANN	Benign	0.30

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: rs11024665; hg19: chr11-18488219;