chr6-29958195-A-T

Variant names:

• chr6-29958195-A-T
• rs2517701

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 0.319 in 152,422 control chromosomes in the GnomAD database, including 8,077 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 0.32 (8047 hom., cov: 32)
  • Exomes 𝑓: 0.32 (30 hom.)
• Consequence: HLA-W intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01
• Publications: 18 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.344 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

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HLA-W	ENST00000439514.1	TSL:6	n.689-144A>T		intron	N/A
	POLR1HASP	ENST00000849678.1		n.589-11279T>A		intron	N/A
	POLR1HASP	ENST00000849679.1		n.65+18408T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.319 AC: 48445 AN: 151802 Hom.: 8045 Cov.: 32

Gnomad AFR AF: 0.283

Gnomad AMI AF: 0.297

Gnomad AMR AF: 0.352

Gnomad ASJ AF: 0.255

Gnomad EAS AF: 0.297

Gnomad SAS AF: 0.219

Gnomad FIN AF: 0.410

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.333

Gnomad OTH AF: 0.299

GnomAD4 exome AF: 0.323 AC: 163 AN: 504 Hom.: 30 AF XY: 0.322 AC XY: 101 AN XY: 314

African (AFR) AF: 0.250 AC: 1 AN: 4

American (AMR) AF: 0.333 AC: 4 AN: 12

Ashkenazi Jewish (ASJ) AF: 0.500 AC: 2 AN: 4

East Asian (EAS) AF: 0.250 AC: 1 AN: 4

South Asian (SAS) AF: 0.321 AC: 9 AN: 28

European-Finnish (FIN) AF: 0.395 AC: 60 AN: 152

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2

European-Non Finnish (NFE) AF: 0.281 AC: 82 AN: 292

Other (OTH) AF: 0.667 AC: 4 AN: 6

GnomAD4 genome AF: 0.319 AC: 48459 AN: 151918 Hom.: 8047 Cov.: 32 AF XY: 0.318 AC XY: 23620 AN XY: 74242

African (AFR) AF: 0.283 AC: 11693 AN: 41360

American (AMR) AF: 0.352 AC: 5375 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.255 AC: 886 AN: 3470

East Asian (EAS) AF: 0.298 AC: 1536 AN: 5160

South Asian (SAS) AF: 0.218 AC: 1049 AN: 4812

European-Finnish (FIN) AF: 0.410 AC: 4335 AN: 10578

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.333 AC: 22606 AN: 67950

Other (OTH) AF: 0.295 AC: 624 AN: 2114

Alfa AF: 0.322 Hom.: 4452

Bravo AF: 0.316

Asia WGS AF: 0.236 AC: 817 AN: 3452

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.5
DANN	Benign	0.52
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs2517701; hg19: chr6-29925972;