rs2023478

Variant names:

• chr6-30261680-C-G
• rs2023478
• ENST00000420110.1:n.988C>G

Your query was ambiguous. Multiple possible variants found:

• chr6-30261680-C-G
• chr6-30261680-C-T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NR_027822.1(HLA-L):​n.875C>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 31)
• Consequence: HLA-L NR_027822.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.164

Genes affected

HLA-L (HGNC:4970): (major histocompatibility complex, class I, L (pseudogene))

HLA-L (HGNC:):

HCG17 (HGNC:31339): (HLA complex group 17)

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HLA-L	NR_027822.1	n.875C>G		non_coding_transcript_exon_variant	Exon 5 of 7
HCG17	NR_052012.1	n.127-7216G>C		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HLA-L	ENST00000420110.1	n.988C>G		non_coding_transcript_exon_variant	Exon 5 of 5	6
HLA-L	ENST00000463348.6	n.884C>G		non_coding_transcript_exon_variant	Exon 5 of 7	6
HLA-L	ENST00000482052.6	n.1102C>G		non_coding_transcript_exon_variant	Exon 4 of 6	6

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Cov.: 22

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	5.0
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2023478; hg19: chr6-30229457;