rs4796119

chr17-35866084-T-C

Variant summary

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

The NM_152781.4(HEATR9):c.138+640A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0945 in 152,254 control chromosomes in the GnomAD database, including 871 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 0.094 (871 hom., cov: 32)
• Consequence: HEATR9 NM_152781.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.400

Genes affected

HEATR9 (HGNC:26548): (HEAT repeat containing 9) Predicted to act upstream of or within hematopoietic progenitor cell differentiation. [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=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.207 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HEATR9	NM_152781.4	c.138+640A>G		intron_variant		ENST00000604834.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HEATR9	ENST00000604834.6	c.138+640A>G		intron_variant		1	NM_152781.4	P2

Frequencies

GnomAD3 genomes AF: 0.0944 AC: 14364 AN: 152136 Hom.: 867 Cov.: 32

Gnomad AFR AF: 0.0356

Gnomad AMI AF: 0.128

Gnomad AMR AF: 0.150

Gnomad ASJ AF: 0.146

Gnomad EAS AF: 0.218

Gnomad SAS AF: 0.114

Gnomad FIN AF: 0.111

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.101

Gnomad OTH AF: 0.104

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

GnomAD4 genome AF: 0.0945 AC: 14384 AN: 152254 Hom.: 871 Cov.: 32 AF XY: 0.0964 AC XY: 7174 AN XY: 74442

Gnomad4 AFR AF: 0.0355

Gnomad4 AMR AF: 0.151

Gnomad4 ASJ AF: 0.146

Gnomad4 EAS AF: 0.218

Gnomad4 SAS AF: 0.115

Gnomad4 FIN AF: 0.111

Gnomad4 NFE AF: 0.101

Gnomad4 OTH AF: 0.103

Alfa AF: 0.108 Hom.: 732

Bravo AF: 0.0983

Asia WGS AF: 0.141 AC: 490 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	4.3
Dann	Benign	0.72

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: rs4796119; hg19: chr17-34193088;