rs389600

Variant names:

• chr6-29929222-C-A
• rs389600
• ENST00000430151.2:n.1036C>A

Your query was ambiguous. Multiple possible variants found:

• chr6-29929222-C-A
• chr6-29929222-C-G
• chr6-29929222-C-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000850440.1(ENSG00000310496):​n.500C>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000625 in 480,064 control chromosomes in the GnomAD database, including 1 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 0.0000078 (0 hom., cov: 24)
  • Exomes 𝑓: 0.0000057 (1 hom.)
• Consequence: ENSG00000310496 ENST00000850440.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -7.51
• Publications: 11 publications found

Genes affected

HLA-K (HGNC:4969): (major histocompatibility complex, class I, K (pseudogene))

ENSG00000310496 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000850440.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HLA-K	ENST00000430151.2	TSL:6	n.1036C>A		non_coding_transcript_exon	Exon 6 of 6
	ENSG00000310496	ENST00000850440.1		n.500C>A		non_coding_transcript_exon	Exon 4 of 5
	ENSG00000310496	ENST00000850441.1		n.438C>A		non_coding_transcript_exon	Exon 4 of 5

Frequencies

GnomAD3 genomes AF: 0.00000777 AC: 1 AN: 128700 Hom.: 0 Cov.: 24

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000161

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.00000569 AC: 2 AN: 351364 Hom.: 1 Cov.: 0 AF XY: 0.0000102 AC XY: 2 AN XY: 196968

African (AFR) AF: 0.00 AC: 0 AN: 9378

American (AMR) AF: 0.0000776 AC: 2 AN: 25764

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 9548

East Asian (EAS) AF: 0.00 AC: 0 AN: 14090

South Asian (SAS) AF: 0.00 AC: 0 AN: 53470

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 29706

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2694

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 189950

Other (OTH) AF: 0.00 AC: 0 AN: 16764

GnomAD4 genome AF: 0.00000777 AC: 1 AN: 128700 Hom.: 0 Cov.: 24 AF XY: 0.0000162 AC XY: 1 AN XY: 61892

African (AFR) AF: 0.00 AC: 0 AN: 32806

American (AMR) AF: 0.00 AC: 0 AN: 11804

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3112

East Asian (EAS) AF: 0.00 AC: 0 AN: 3854

South Asian (SAS) AF: 0.00 AC: 0 AN: 3656

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 8602

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 272

European-Non Finnish (NFE) AF: 0.0000161 AC: 1 AN: 62012

Other (OTH) AF: 0.00 AC: 0 AN: 1742

Alfa AF: 0.00 Hom.: 104

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.83
DANN	Benign	0.62
PhyloP100		-7.5

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs389600;

hg19: chr6-29896999;