rs10229603

Positions:

• chr7-112988318-T-C

Variant summary

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

The ENST00000447785.1(HRAT17):​n.61-7157A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.303 in 152,072 control chromosomes in the GnomAD database, including 7,187 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 0.30 (7187 hom., cov: 32)
• Consequence: HRAT17 ENST00000447785.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0800

Genes affected

HRAT17 (HGNC:):

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 (SAS) allele frequency at 95% confidence interval = 0.41 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
HRAT17	NR_110162.1	n.77-1654A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HRAT17	ENST00000447785.1	n.61-7157A>G		intron_variant		4
HRAT17	ENST00000451962.5	n.68-1654A>G		intron_variant		5
HRAT17	ENST00000653138.2	n.129+7250A>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.303 AC: 46020 AN: 151954 Hom.: 7173 Cov.: 32

Gnomad AFR AF: 0.332

Gnomad AMI AF: 0.300

Gnomad AMR AF: 0.250

Gnomad ASJ AF: 0.322

Gnomad EAS AF: 0.207

Gnomad SAS AF: 0.425

Gnomad FIN AF: 0.298

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.295

Gnomad OTH AF: 0.308

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

GnomAD4 genome AF: 0.303 AC: 46069 AN: 152072 Hom.: 7187 Cov.: 32 AF XY: 0.305 AC XY: 22673 AN XY: 74334

Gnomad4 AFR AF: 0.332

Gnomad4 AMR AF: 0.250

Gnomad4 ASJ AF: 0.322

Gnomad4 EAS AF: 0.207

Gnomad4 SAS AF: 0.425

Gnomad4 FIN AF: 0.298

Gnomad4 NFE AF: 0.295

Gnomad4 OTH AF: 0.314

Alfa AF: 0.299 Hom.: 11877

Bravo AF: 0.297

Asia WGS AF: 0.326 AC: 1136 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	1.2
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10229603; hg19: chr7-112628373;