rs2541675

Variant names:

• chr16-168736-A-G
• rs2541675
• ENST00000438841.1:n.58A>G

Your query was ambiguous. Multiple possible variants found:

• chr16-168736-A-G
• chr16-168736-A-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
HBAP1		n.168736A>G		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HBAP1	ENST00000438841.1	n.58A>G		non_coding_transcript_exon_variant	Exon 1 of 3	6

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

African (AFR) AF: 1.00 AC: 2 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AF: 0.500 AC: 1 AN: 2

European-Finnish (FIN) AF: 0.750 AC: 3 AN: 4

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.617 AC: 37 AN: 60

Other (OTH) AF: 0.500 AC: 2 AN: 4

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

African (AFR) AF: 0.945 AC: 39225 AN: 41516

American (AMR) AF: 0.717 AC: 10944 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.726 AC: 2519 AN: 3472

East Asian (EAS) AF: 0.527 AC: 2709 AN: 5138

South Asian (SAS) AF: 0.711 AC: 3425 AN: 4816

European-Finnish (FIN) AF: 0.661 AC: 6984 AN: 10570

Middle Eastern (MID) AF: 0.752 AC: 221 AN: 294

European-Non Finnish (NFE) AF: 0.724 AC: 49205 AN: 67968

Other (OTH) AF: 0.734 AC: 1548 AN: 2108

Alfa AF: 0.813 Hom.: 17067

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
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs2541675; hg19: chr16-218735;