chr1-89601247-G-A

Position:

• chr1-89601247-G-A

Variant summary

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

The ENST00000655657.3(LRRC8C-DT):​n.518-13162C>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 0.355 in 152,034 control chromosomes in the GnomAD database, including 9,636 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 0.35 (9636 hom., cov: 32)
• Consequence: LRRC8C-DT ENST00000655657.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.215

Genes affected

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

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 (AFR) allele frequency at 95% confidence interval = 0.373 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
LRRC8C-DT	ENST00000655657.3	n.518-13162C>T		intron_variant, non_coding_transcript_variant
LRRC8C-DT	ENST00000443562.2	n.177-3043C>T		intron_variant, non_coding_transcript_variant		3
LRRC8C-DT	ENST00000666228.1	n.219-13162C>T		intron_variant, non_coding_transcript_variant
LRRC8C-DT	ENST00000702838.1	n.446-3043C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.355 AC: 53913 AN: 151914 Hom.: 9625 Cov.: 32

Gnomad AFR AF: 0.379

Gnomad AMI AF: 0.211

Gnomad AMR AF: 0.326

Gnomad ASJ AF: 0.346

Gnomad EAS AF: 0.223

Gnomad SAS AF: 0.341

Gnomad FIN AF: 0.435

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.349

Gnomad OTH AF: 0.328

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

GnomAD4 genome AF: 0.355 AC: 53948 AN: 152034 Hom.: 9636 Cov.: 32 AF XY: 0.359 AC XY: 26697 AN XY: 74322

Gnomad4 AFR AF: 0.378

Gnomad4 AMR AF: 0.326

Gnomad4 ASJ AF: 0.346

Gnomad4 EAS AF: 0.223

Gnomad4 SAS AF: 0.341

Gnomad4 FIN AF: 0.435

Gnomad4 NFE AF: 0.349

Gnomad4 OTH AF: 0.332

Alfa AF: 0.345 Hom.: 12201

Bravo AF: 0.347

Asia WGS AF: 0.314 AC: 1091 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.68
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1215494; hg19: chr1-90066806;