rs9312006

Variant names:

• chr3-8217804-A-C
• rs9312006
• ENST00000446281.5:n.515-225502T>G

Your query was ambiguous. Multiple possible variants found:

• chr3-8217804-A-C
• chr3-8217804-A-T

Variant summary

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

The ENST00000452802.6(LMCD1-AS1):​n.583-22731T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.594 in 151,960 control chromosomes in the GnomAD database, including 27,402 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 0.59 (27402 hom., cov: 32)
• Consequence: LMCD1-AS1 ENST00000452802.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.270

Genes affected

LMCD1-AS1 (HGNC:44477): (LMCD1 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.742 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LMCD1-AS1	ENST00000446281.5	n.515-225502T>G		intron_variant	Intron 3 of 5	5
LMCD1-AS1	ENST00000452802.6	n.583-22731T>G		intron_variant	Intron 3 of 3	2
LMCD1-AS1	ENST00000654635.1	n.589-22731T>G		intron_variant	Intron 3 of 6
LMCD1-AS1	ENST00000659617.1	n.597-22731T>G		intron_variant	Intron 3 of 6

Frequencies

GnomAD3 genomes AF: 0.594 AC: 90127 AN: 151842 Hom.: 27362 Cov.: 32

Gnomad AFR AF: 0.710

Gnomad AMI AF: 0.590

Gnomad AMR AF: 0.537

Gnomad ASJ AF: 0.472

Gnomad EAS AF: 0.762

Gnomad SAS AF: 0.662

Gnomad FIN AF: 0.585

Gnomad MID AF: 0.599

Gnomad NFE AF: 0.526

Gnomad OTH AF: 0.575

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

GnomAD4 genome AF: 0.594 AC: 90219 AN: 151960 Hom.: 27402 Cov.: 32 AF XY: 0.598 AC XY: 44405 AN XY: 74274

Gnomad4 AFR AF: 0.710

Gnomad4 AMR AF: 0.536

Gnomad4 ASJ AF: 0.472

Gnomad4 EAS AF: 0.762

Gnomad4 SAS AF: 0.662

Gnomad4 FIN AF: 0.585

Gnomad4 NFE AF: 0.526

Gnomad4 OTH AF: 0.579

Alfa AF: 0.530 Hom.: 34538

Bravo AF: 0.597

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.3
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9312006; hg19: chr3-8259491;