rs1291362

Variant names:

• chr12-13001977-A-G
• rs1291362
• ENST00000538670.1:n.479A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 15 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=-0.64).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.649 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_002774.3. 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.1536A>G		non_coding_transcript_exon	Exon 1 of 1
	GPRC5D-AS1	NR_149067.1		n.178-20037A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	HTR7P1	ENST00000538670.1	TSL:6	n.479A>G		non_coding_transcript_exon	Exon 1 of 1
	HTR7P1	ENST00000624664.1	TSL:6	n.1558A>G		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000255621	ENST00000543321.1	TSL:5	n.31+1496A>G		intron	N/A

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

African (AFR) AF: 0.583 AC: 10258 AN: 17598

American (AMR) AF: 0.553 AC: 20118 AN: 36410

Ashkenazi Jewish (ASJ) AF: 0.561 AC: 10738 AN: 19142

East Asian (EAS) AF: 0.518 AC: 17306 AN: 33408

South Asian (SAS) AF: 0.648 AC: 43056 AN: 66432

European-Finnish (FIN) AF: 0.655 AC: 31711 AN: 48408

Middle Eastern (MID) AF: 0.560 AC: 2307 AN: 4122

European-Non Finnish (NFE) AF: 0.622 AC: 236315 AN: 380148

Other (OTH) AF: 0.597 AC: 19115 AN: 32036

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

African (AFR) AF: 0.587 AC: 24333 AN: 41420

American (AMR) AF: 0.528 AC: 8067 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.579 AC: 2010 AN: 3470

East Asian (EAS) AF: 0.523 AC: 2693 AN: 5154

South Asian (SAS) AF: 0.668 AC: 3217 AN: 4814

European-Finnish (FIN) AF: 0.653 AC: 6912 AN: 10578

Middle Eastern (MID) AF: 0.476 AC: 140 AN: 294

European-Non Finnish (NFE) AF: 0.647 AC: 43948 AN: 67954

Other (OTH) AF: 0.571 AC: 1205 AN: 2110

Alfa AF: 0.628 Hom.: 25733

Bravo AF: 0.597

Asia WGS AF: 0.581 AC: 2021 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	12
DANN	Benign	0.64
PhyloP100		3.5

Splicing

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

Other links and lift over

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