rs2541675

chr16-168736-A-Gchr16-168736-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000438841.1(HBAP1):n.58A>G 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 0.773 in 152,134 control chromosomes in the GnomAD database, including 46,387 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 0.77 (46373 hom., cov: 32)
  • Exomes 𝑓: 0.63 (14 hom.)
• Consequence: HBAP1 ENST00000438841.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.68

Genes affected

HBAP1 (HGNC:4825): (hemoglobin subunit alpha pseudogene 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.937 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HBAP1	ENST00000438841.1	n.58A>G		non_coding_transcript_exon_variant	1/3

Frequencies

GnomAD3 genomes AF: 0.773 AC: 117379 AN: 151942 Hom.: 46310 Cov.: 32

Gnomad AFR AF: 0.945

Gnomad AMI AF: 0.794

Gnomad AMR AF: 0.717

Gnomad ASJ AF: 0.726

Gnomad EAS AF: 0.528

Gnomad SAS AF: 0.711

Gnomad FIN AF: 0.661

Gnomad MID AF: 0.759

Gnomad NFE AF: 0.724

Gnomad OTH AF: 0.731

GnomAD4 exome AF: 0.625 AC: 45 AN: 72 Hom.: 14 Cov.: 0 AF XY: 0.593 AC XY: 32 AN XY: 54

Gnomad4 AFR exome AF: 1.00

Gnomad4 SAS exome AF: 0.500

Gnomad4 FIN exome AF: 0.750

Gnomad4 NFE exome AF: 0.617

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.773 AC: 117501 AN: 152062 Hom.: 46373 Cov.: 32 AF XY: 0.765 AC XY: 56873 AN XY: 74314

Gnomad4 AFR AF: 0.945

Gnomad4 AMR AF: 0.717

Gnomad4 ASJ AF: 0.726

Gnomad4 EAS AF: 0.527

Gnomad4 SAS AF: 0.711

Gnomad4 FIN AF: 0.661

Gnomad4 NFE AF: 0.724

Gnomad4 OTH AF: 0.734

Alfa AF: 0.771 Hom.: 10869

Bravo AF: 0.784

Asia WGS AF: 0.668 AC: 2320 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.23
Dann	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2541675; hg19: chr16-218735;