rs6945242

Positions:

• chr7-32934206-C-A
• chr7-32934206-C-G

Variant summary

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

The NR_003500.2(RP9P):​n.340-310G>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.145 in 151,848 control chromosomes in the GnomAD database, including 1,661 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 0.15 (1661 hom., cov: 31)
• Consequence: RP9P NR_003500.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.855

Genes affected

RP9P (HGNC:33969): (RP9 pseudogene)

ACMG classification

Verdict is Benign. Variant got -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 = 0.174 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RP9P	NR_003500.2	n.340-310G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RP9P	ENST00000381639.3	n.308-310G>T		intron_variant, non_coding_transcript_variant		1
RP9P	ENST00000450133.5	n.170-4098G>T		intron_variant, non_coding_transcript_variant
RP9P	ENST00000685019.1	n.233-4098G>T		intron_variant, non_coding_transcript_variant
RP9P	ENST00000702940.1	n.263-310G>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.145 AC: 22031 AN: 151726 Hom.: 1660 Cov.: 31

Gnomad AFR AF: 0.119

Gnomad AMI AF: 0.0637

Gnomad AMR AF: 0.129

Gnomad ASJ AF: 0.204

Gnomad EAS AF: 0.0587

Gnomad SAS AF: 0.184

Gnomad FIN AF: 0.117

Gnomad MID AF: 0.220

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.177

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.145 AC: 22039 AN: 151848 Hom.: 1661 Cov.: 31 AF XY: 0.142 AC XY: 10555 AN XY: 74224

Gnomad4 AFR AF: 0.118

Gnomad4 AMR AF: 0.129

Gnomad4 ASJ AF: 0.204

Gnomad4 EAS AF: 0.0588

Gnomad4 SAS AF: 0.184

Gnomad4 FIN AF: 0.117

Gnomad4 NFE AF: 0.170

Gnomad4 OTH AF: 0.176

Alfa AF: 0.164 Hom.: 2526

Bravo AF: 0.141

Asia WGS AF: 0.134 AC: 467 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	0.88
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6945242; hg19: chr7-32973818;