rs1291362

chr12-13001977-A-G

Variant summary

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

The NR_002774.3(HTR7P1):n.1536A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.613 in 789,688 control chromosomes in the GnomAD database, including 149,645 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 0.61 (28632 hom., cov: 31)
  • Exomes 𝑓: 0.61 (121013 hom.)
• Consequence: HTR7P1 NR_002774.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.47

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=-0.64).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.649 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
HTR7P1	NR_002774.3	n.1536A>G		non_coding_transcript_exon_variant	1/1
GPRC5D-AS1	NR_149067.1	n.178-20037A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HTR7P1	ENST00000538670.1	n.479A>G		non_coding_transcript_exon_variant	1/1
HTR7P1	ENST00000624664.1	n.1558A>G		non_coding_transcript_exon_variant	1/1
	ENST00000543321.1	n.31+1496A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.612 AC: 92900 AN: 151866 Hom.: 28621 Cov.: 31

Gnomad AFR AF: 0.588

Gnomad AMI AF: 0.464

Gnomad AMR AF: 0.528

Gnomad ASJ AF: 0.579

Gnomad EAS AF: 0.522

Gnomad SAS AF: 0.669

Gnomad FIN AF: 0.653

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.647

Gnomad OTH AF: 0.573

GnomAD4 exome AF: 0.613 AC: 390924 AN: 637704 Hom.: 121013 Cov.: 8 AF XY: 0.616 AC XY: 211505 AN XY: 343486

Gnomad4 AFR exome AF: 0.583

Gnomad4 AMR exome AF: 0.553

Gnomad4 ASJ exome AF: 0.561

Gnomad4 EAS exome AF: 0.518

Gnomad4 SAS exome AF: 0.648

Gnomad4 FIN exome AF: 0.655

Gnomad4 NFE exome AF: 0.622

Gnomad4 OTH exome AF: 0.597

GnomAD4 genome AF: 0.612 AC: 92947 AN: 151984 Hom.: 28632 Cov.: 31 AF XY: 0.610 AC XY: 45280 AN XY: 74280

Gnomad4 AFR AF: 0.587

Gnomad4 AMR AF: 0.528

Gnomad4 ASJ AF: 0.579

Gnomad4 EAS AF: 0.523

Gnomad4 SAS AF: 0.668

Gnomad4 FIN AF: 0.653

Gnomad4 NFE AF: 0.647

Gnomad4 OTH AF: 0.571

Alfa AF: 0.634 Hom.: 18588

Bravo AF: 0.597

Asia WGS AF: 0.581 AC: 2021 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
Cadd	Benign	12
Dann	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1291362; hg19: chr12-13154911; COSMIC: COSV50009526;