rs1215512

Positions:

• chr1-89621952-C-A
• chr1-89621952-C-T

Variant summary

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

The ENST00000655657.3(LRRC8C-DT):​n.517+10064G>T 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 0.523 in 151,970 control chromosomes in the GnomAD database, including 21,999 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 0.52 (21999 hom., cov: 32)
• Consequence: LRRC8C-DT ENST00000655657.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.610

Genes affected

LRRC8C-DT (HGNC:53731): (LRRC8C divergent transcript)

LRRC8C (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.717 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LRRC8C	XM_011542282.3	c.-5+5918C>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LRRC8C-DT	ENST00000655657.3	n.517+10064G>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.523 AC: 79400 AN: 151852 Hom.: 21961 Cov.: 32

Gnomad AFR AF: 0.698

Gnomad AMI AF: 0.281

Gnomad AMR AF: 0.512

Gnomad ASJ AF: 0.445

Gnomad EAS AF: 0.736

Gnomad SAS AF: 0.352

Gnomad FIN AF: 0.379

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.445

Gnomad OTH AF: 0.506

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

GnomAD4 genome AF: 0.523 AC: 79492 AN: 151970 Hom.: 21999 Cov.: 32 AF XY: 0.519 AC XY: 38564 AN XY: 74274

Gnomad4 AFR AF: 0.698

Gnomad4 AMR AF: 0.512

Gnomad4 ASJ AF: 0.445

Gnomad4 EAS AF: 0.736

Gnomad4 SAS AF: 0.354

Gnomad4 FIN AF: 0.379

Gnomad4 NFE AF: 0.445

Gnomad4 OTH AF: 0.504

Alfa AF: 0.456 Hom.: 17031

Bravo AF: 0.545

Asia WGS AF: 0.533 AC: 1855 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.2
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1215512; hg19: chr1-90087511;