12-13002232-G-T

Position:

• chr12-13002232-G-T

Variant summary

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

The NR_002774.3(HTR7P1):​n.1791G>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 NR_002774.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 6.97

Genes affected

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

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
HTR7P1	NR_002774.3	n.1791G>T		non_coding_transcript_exon_variant	1/1
GPRC5D-AS1	NR_149067.1	n.178-19782G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
HTR7P1	ENST00000538670.1	n.734G>T		non_coding_transcript_exon_variant	1/1
HTR7P1	ENST00000624664.1	n.1813G>T		non_coding_transcript_exon_variant	1/1
	ENST00000543321.1	n.31+1751G>T		intron_variant, non_coding_transcript_variant		5

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

Gnomad4 AFR exome AF: 0.237

Gnomad4 AMR exome AF: 0.290

Gnomad4 ASJ exome AF: 0.514

Gnomad4 EAS exome AF: 0.337

Gnomad4 SAS exome AF: 0.598

Gnomad4 FIN exome AF: 0.581

Gnomad4 NFE exome AF: 0.614

Gnomad4 OTH exome AF: 0.534

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

Gnomad4 AFR AF: 0.247

Gnomad4 AMR AF: 0.379

Gnomad4 ASJ AF: 0.551

Gnomad4 EAS AF: 0.366

Gnomad4 SAS AF: 0.611

Gnomad4 FIN AF: 0.598

Gnomad4 NFE AF: 0.637

Gnomad4 OTH AF: 0.472

Alfa AF: 0.586 Hom.: 12870

Bravo AF: 0.452

Asia WGS AF: 0.430 AC: 1496 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

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