rs892666

Variant names:

• chr6-29956951-T-C
• rs892666

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.645 in 150,694 control chromosomes in the GnomAD database, including 31,457 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 0.65 (31446 hom., cov: 30)
  • Exomes 𝑓: 0.58 (11 hom.)
• Consequence: HLA-W intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.22
• Publications: 11 publications found

Genes affected

HLA-W (HGNC:23425): (major histocompatibility complex, class I, W (pseudogene))

POLR1HASP (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.666 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000439514.1. 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-W	ENST00000439514.1	TSL:6	n.261+95T>C		intron	N/A
	POLR1HASP	ENST00000849678.1		n.589-10035A>G		intron	N/A
	POLR1HASP	ENST00000849679.1		n.65+19652A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.645 AC: 97118 AN: 150520 Hom.: 31430 Cov.: 30

Gnomad AFR AF: 0.654

Gnomad AMI AF: 0.729

Gnomad AMR AF: 0.605

Gnomad ASJ AF: 0.557

Gnomad EAS AF: 0.551

Gnomad SAS AF: 0.532

Gnomad FIN AF: 0.627

Gnomad MID AF: 0.605

Gnomad NFE AF: 0.671

Gnomad OTH AF: 0.633

GnomAD4 exome AF: 0.581 AC: 36 AN: 62 Hom.: 11 AF XY: 0.571 AC XY: 24 AN XY: 42

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 0.500 AC: 1 AN: 2

East Asian (EAS) AF: 0.00 AC: 0 AN: 2

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.500 AC: 3 AN: 6

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.571 AC: 24 AN: 42

Other (OTH) AF: 0.800 AC: 8 AN: 10

GnomAD4 genome AF: 0.645 AC: 97163 AN: 150632 Hom.: 31446 Cov.: 30 AF XY: 0.640 AC XY: 47079 AN XY: 73612

African (AFR) AF: 0.654 AC: 26545 AN: 40604

American (AMR) AF: 0.604 AC: 9121 AN: 15110

Ashkenazi Jewish (ASJ) AF: 0.557 AC: 1922 AN: 3448

East Asian (EAS) AF: 0.551 AC: 2814 AN: 5110

South Asian (SAS) AF: 0.531 AC: 2552 AN: 4802

European-Finnish (FIN) AF: 0.627 AC: 6600 AN: 10532

Middle Eastern (MID) AF: 0.592 AC: 173 AN: 292

European-Non Finnish (NFE) AF: 0.671 AC: 45462 AN: 67738

Other (OTH) AF: 0.628 AC: 1309 AN: 2084

Alfa AF: 0.662 Hom.: 35438

Bravo AF: 0.652

Asia WGS AF: 0.507 AC: 1759 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.8
DANN	Benign	0.47
PhyloP100		-3.2

Splicing

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

Other links and lift over

dbSNP: rs892666; hg19: chr6-29924728;