ENST00000438841.1:n.-146T>C

Variant names:

• chr16-168533-T-C
• rs1203833
• ENST00000438841.1:n.-146T>C

Variant summary

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

The ENST00000438841.1(HBAP1):​n.-146T>C variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.206 in 152,092 control chromosomes in the GnomAD database, including 3,360 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 0.21 (3359 hom., cov: 32)
  • Exomes 𝑓: 0.24 (1 hom.)
• Consequence: HBAP1 ENST00000438841.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.77
• 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 (SAS) allele frequency at 95% confidence interval = 0.265 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HBAP1	ENST00000438841.1	n.-146T>C		upstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.206 AC: 31293 AN: 151870 Hom.: 3357 Cov.: 32

Gnomad AFR AF: 0.252

Gnomad AMI AF: 0.249

Gnomad AMR AF: 0.215

Gnomad ASJ AF: 0.225

Gnomad EAS AF: 0.181

Gnomad SAS AF: 0.279

Gnomad FIN AF: 0.147

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.180

Gnomad OTH AF: 0.207

GnomAD4 exome AF: 0.240 AC: 24 AN: 100 Hom.: 1 AF XY: 0.250 AC XY: 18 AN XY: 72

African (AFR) AF: 0.00 AC: 0 AN: 6

American (AMR) AF: 0.00 AC: 0 AN: 2

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AF: 0.500 AC: 2 AN: 4

European-Finnish (FIN) AF: 0.250 AC: 2 AN: 8

Middle Eastern (MID) AF: 1.00 AC: 2 AN: 2

European-Non Finnish (NFE) AF: 0.237 AC: 18 AN: 76

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.206 AC: 31318 AN: 151992 Hom.: 3359 Cov.: 32 AF XY: 0.205 AC XY: 15245 AN XY: 74312

African (AFR) AF: 0.252 AC: 10437 AN: 41438

American (AMR) AF: 0.215 AC: 3282 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.225 AC: 782 AN: 3468

East Asian (EAS) AF: 0.181 AC: 931 AN: 5150

South Asian (SAS) AF: 0.278 AC: 1336 AN: 4814

European-Finnish (FIN) AF: 0.147 AC: 1558 AN: 10594

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.180 AC: 12249 AN: 67952

Other (OTH) AF: 0.209 AC: 442 AN: 2114

Alfa AF: 0.200 Hom.: 977

Bravo AF: 0.213

Asia WGS AF: 0.262 AC: 913 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	0.27
DANN	Benign	0.44
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs1203833; hg19: chr16-218532; COSMIC: COSV52406424;