rs9312006

Positions:

• 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 ENST00000654635.1(LMCD1-AS1):​n.589-22731T>G variant causes a intron, non coding transcript 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 ENST00000654635.1 intron, non_coding_transcript
• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LMCD1-AS1	ENST00000654635.1	n.589-22731T>G		intron_variant, non_coding_transcript_variant
LMCD1-AS1	ENST00000446281.5	n.515-225502T>G		intron_variant, non_coding_transcript_variant		5
LMCD1-AS1	ENST00000452802.6	n.583-22731T>G		intron_variant, non_coding_transcript_variant		2
LMCD1-AS1	ENST00000659617.1	n.597-22731T>G		intron_variant, non_coding_transcript_variant

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;