ENST00000538670.1:n.734G>T

Variant names:

• chr12-13002232-G-T
• rs1291361
• ENST00000538670.1:n.734G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000538670.1(HTR7P1):​n.734G>T variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.538 in 574,542 control chromosomes in the GnomAD database, including 89,212 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 0.49 (20364 hom., cov: 32)
  • Exomes 𝑓: 0.56 (68848 hom.)
• Consequence: HTR7P1 ENST00000538670.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 6.97
• Publications: 18 publications found

Genes affected

HTR7P1 (HGNC:30411): (5-hydroxytryptamine receptor 7 pseudogene 1)

HTR7P1 (HGNC:):

GPRC5D-AS1 (HGNC:53599): (GPRC5D and HEBP1 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.53).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.632 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000538670.1. 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
	HTR7P1	NR_002774.3		n.1791G>T		non_coding_transcript_exon	Exon 1 of 1
	GPRC5D-AS1	NR_149067.1		n.178-19782G>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HTR7P1	ENST00000538670.1	TSL:6	n.734G>T		non_coding_transcript_exon	Exon 1 of 1
	HTR7P1	ENST00000624664.1	TSL:6	n.1813G>T		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000255621	ENST00000543321.1	TSL:5	n.31+1751G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.487 AC: 73944 AN: 151888 Hom.: 20371 Cov.: 32

Gnomad AFR AF: 0.247

Gnomad AMI AF: 0.463

Gnomad AMR AF: 0.380

Gnomad ASJ AF: 0.551

Gnomad EAS AF: 0.366

Gnomad SAS AF: 0.612

Gnomad FIN AF: 0.598

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.637

Gnomad OTH AF: 0.475

GnomAD4 exome AF: 0.556 AC: 234923 AN: 422536 Hom.: 68848 Cov.: 2 AF XY: 0.563 AC XY: 130025 AN XY: 231044

African (AFR) AF: 0.237 AC: 2924 AN: 12312

American (AMR) AF: 0.290 AC: 6602 AN: 22800

Ashkenazi Jewish (ASJ) AF: 0.514 AC: 5817 AN: 11310

East Asian (EAS) AF: 0.337 AC: 8952 AN: 26538

South Asian (SAS) AF: 0.598 AC: 29018 AN: 48492

European-Finnish (FIN) AF: 0.581 AC: 21314 AN: 36676

Middle Eastern (MID) AF: 0.524 AC: 1694 AN: 3232

European-Non Finnish (NFE) AF: 0.614 AC: 146600 AN: 238694

Other (OTH) AF: 0.534 AC: 12002 AN: 22482

GnomAD4 genome AF: 0.486 AC: 73930 AN: 152006 Hom.: 20364 Cov.: 32 AF XY: 0.484 AC XY: 35952 AN XY: 74292

African (AFR) AF: 0.247 AC: 10235 AN: 41472

American (AMR) AF: 0.379 AC: 5795 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.551 AC: 1911 AN: 3470

East Asian (EAS) AF: 0.366 AC: 1883 AN: 5150

South Asian (SAS) AF: 0.611 AC: 2944 AN: 4818

European-Finnish (FIN) AF: 0.598 AC: 6310 AN: 10552

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.637 AC: 43300 AN: 67944

Other (OTH) AF: 0.472 AC: 996 AN: 2110

Alfa AF: 0.566 Hom.: 22210

Bravo AF: 0.452

Asia WGS AF: 0.430 AC: 1496 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.53
CADD	Benign	12
DANN	Benign	0.74
PhyloP100		7.0

Splicing

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

Other links and lift over

dbSNP: rs1291361; hg19: chr12-13155166; COSMIC: COSV50009754;