rs4796119

Variant names:

• chr17-35866084-T-C
• rs4796119
• NM_152781.4:c.138+640A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 8 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_152781.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HEATR9	NM_152781.4	MANE Select	c.138+640A>G		intron	N/A	NP_689994.2	A2RTY3-1
	HEATR9	NM_001321395.2		c.138+640A>G		intron	N/A	NP_001308324.1	A2RTY3-3
	HEATR9	NR_135630.2		n.287+640A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HEATR9	ENST00000604834.6	TSL:1 MANE Select	c.138+640A>G		intron	N/A	ENSP00000473941.1	A2RTY3-1
	HEATR9	ENST00000603323.5	TSL:1	n.138+640A>G		intron	N/A	ENSP00000474391.1	A0A075B7D3
	HEATR9	ENST00000603870.5	TSL:2	c.138+640A>G		intron	N/A	ENSP00000473760.1	A2RTY3-3

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

African (AFR) AF: 0.0355 AC: 1474 AN: 41554

American (AMR) AF: 0.151 AC: 2311 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.146 AC: 505 AN: 3464

East Asian (EAS) AF: 0.218 AC: 1128 AN: 5184

South Asian (SAS) AF: 0.115 AC: 555 AN: 4828

European-Finnish (FIN) AF: 0.111 AC: 1172 AN: 10596

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.101 AC: 6858 AN: 68030

Other (OTH) AF: 0.103 AC: 217 AN: 2108

Alfa AF: 0.106 Hom.: 1009

Bravo AF: 0.0983

Asia WGS AF: 0.141 AC: 490 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.3
DANN	Benign	0.72
PhyloP100		0.40

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

Other links and lift over

dbSNP: rs4796119; hg19: chr17-34193088;