8-132102752-C-T

Position:

• chr8-132102752-C-T

Variant summary

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

The NM_001145095.3(HHLA1):​c.139+1356G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.604 in 151,250 control chromosomes in the GnomAD database, including 27,682 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 0.60 (27682 hom., cov: 29)
• Consequence: HHLA1 NM_001145095.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04

Genes affected

HHLA1 (HGNC:4904): (HHLA1 neighbor of OC90) Predicted to be located in extracellular region. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.638 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
HHLA1	NM_001145095.3	c.139+1356G>A		intron_variant		ENST00000414222.2	NP_001138567.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HHLA1	ENST00000414222.2	c.139+1356G>A		intron_variant		5	NM_001145095.3	ENSP00000388322	P2
HHLA1	ENST00000673615.1	c.174+1321G>A		intron_variant				ENSP00000500443	A2

Frequencies

GnomAD3 genomes AF: 0.604 AC: 91233 AN: 151140 Hom.: 27660 Cov.: 29

Gnomad AFR AF: 0.645

Gnomad AMI AF: 0.349

Gnomad AMR AF: 0.639

Gnomad ASJ AF: 0.572

Gnomad EAS AF: 0.464

Gnomad SAS AF: 0.487

Gnomad FIN AF: 0.629

Gnomad MID AF: 0.633

Gnomad NFE AF: 0.592

Gnomad OTH AF: 0.573

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.604 AC: 91302 AN: 151250 Hom.: 27682 Cov.: 29 AF XY: 0.603 AC XY: 44513 AN XY: 73786

Gnomad4 AFR AF: 0.644

Gnomad4 AMR AF: 0.639

Gnomad4 ASJ AF: 0.572

Gnomad4 EAS AF: 0.464

Gnomad4 SAS AF: 0.487

Gnomad4 FIN AF: 0.629

Gnomad4 NFE AF: 0.592

Gnomad4 OTH AF: 0.569

Alfa AF: 0.550 Hom.: 3572

Bravo AF: 0.608

Asia WGS AF: 0.485 AC: 1686 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.56
DANN	Benign	0.76

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs715257; hg19: chr8-133114999;