chr6-31464097-G-T

Variant names:

• chr6-31464097-G-T
• rs2395030
• ENST00000541196.3:n.242G>T

Variant summary

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

The ENST00000541196.3(HCP5):​n.242G>T 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 0.0517 in 343,264 control chromosomes in the GnomAD database, including 758 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 0.040 (223 hom., cov: 32)
  • Exomes 𝑓: 0.061 (535 hom.)
• Consequence: HCP5 ENST00000541196.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.211
• Publications: 10 publications found

Genes affected

HCP5 (HGNC:21659): (HLA complex P5)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0952 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HCP5	NR_040662.1	n.827G>T		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HCP5	ENST00000541196.3	n.242G>T		non_coding_transcript_exon_variant	Exon 3 of 4	1
HCP5	ENST00000414046.3	n.837G>T		non_coding_transcript_exon_variant	Exon 2 of 2	4
HCP5	ENST00000670109.1	n.800G>T		non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0398 AC: 6043 AN: 151886 Hom.: 225 Cov.: 32

Gnomad AFR AF: 0.00804

Gnomad AMI AF: 0.0275

Gnomad AMR AF: 0.0396

Gnomad ASJ AF: 0.0692

Gnomad EAS AF: 0.0791

Gnomad SAS AF: 0.102

Gnomad FIN AF: 0.0556

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0473

Gnomad OTH AF: 0.0560

GnomAD2 exomes AF: 0.0517 AC: 6842 AN: 132220 AF XY: 0.0571

Gnomad AFR exome AF: 0.00700

Gnomad AMR exome AF: 0.0305

Gnomad ASJ exome AF: 0.0702

Gnomad EAS exome AF: 0.0641

Gnomad FIN exome AF: 0.0516

Gnomad NFE exome AF: 0.0520

Gnomad OTH exome AF: 0.0631

GnomAD4 exome AF: 0.0613 AC: 11717 AN: 191260 Hom.: 535 Cov.: 0 AF XY: 0.0696 AC XY: 7490 AN XY: 107602

African (AFR) AF: 0.00696 AC: 26 AN: 3736

American (AMR) AF: 0.0290 AC: 334 AN: 11528

Ashkenazi Jewish (ASJ) AF: 0.0795 AC: 270 AN: 3396

East Asian (EAS) AF: 0.0723 AC: 414 AN: 5728

South Asian (SAS) AF: 0.117 AC: 4089 AN: 34814

European-Finnish (FIN) AF: 0.0520 AC: 1366 AN: 26274

Middle Eastern (MID) AF: 0.127 AC: 265 AN: 2094

European-Non Finnish (NFE) AF: 0.0475 AC: 4545 AN: 95644

Other (OTH) AF: 0.0507 AC: 408 AN: 8046

GnomAD4 genome AF: 0.0397 AC: 6042 AN: 152004 Hom.: 223 Cov.: 32 AF XY: 0.0418 AC XY: 3106 AN XY: 74350

African (AFR) AF: 0.00797 AC: 330 AN: 41404

American (AMR) AF: 0.0395 AC: 601 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.0692 AC: 240 AN: 3466

East Asian (EAS) AF: 0.0795 AC: 410 AN: 5160

South Asian (SAS) AF: 0.103 AC: 495 AN: 4820

European-Finnish (FIN) AF: 0.0556 AC: 590 AN: 10602

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.0473 AC: 3214 AN: 68004

Other (OTH) AF: 0.0549 AC: 116 AN: 2112

Alfa AF: 0.0398 Hom.: 327

Bravo AF: 0.0359

Asia WGS AF: 0.0640 AC: 222 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.4
DANN	Benign	0.32
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs2395030; hg19: chr6-31431874;