rs10229603

Variant names:

• chr7-112988318-T-C
• rs10229603
• ENST00000447785.1:n.61-7157A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 12 publications found

Genes affected

HRAT17 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
HRAT17	NR_110162.1	n.77-1654A>G		intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HRAT17	ENST00000447785.1	n.61-7157A>G		intron_variant	Intron 1 of 4	4
HRAT17	ENST00000451962.6	n.68-1654A>G		intron_variant	Intron 1 of 5	5
HRAT17	ENST00000653138.2	n.129+7250A>G		intron_variant	Intron 1 of 2

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

African (AFR) AF: 0.332 AC: 13771 AN: 41504

American (AMR) AF: 0.250 AC: 3815 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.322 AC: 1116 AN: 3468

East Asian (EAS) AF: 0.207 AC: 1068 AN: 5148

South Asian (SAS) AF: 0.425 AC: 2047 AN: 4816

European-Finnish (FIN) AF: 0.298 AC: 3152 AN: 10584

Middle Eastern (MID) AF: 0.401 AC: 117 AN: 292

European-Non Finnish (NFE) AF: 0.295 AC: 20047 AN: 67962

Other (OTH) AF: 0.314 AC: 663 AN: 2112

Alfa AF: 0.300 Hom.: 17286

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
PhyloP100		-0.080

Splicing

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

Other links and lift over

dbSNP: rs10229603; hg19: chr7-112628373;