rs6945242

Variant names:

• chr7-32934206-C-A
• rs6945242
• ENST00000381639.3:n.308-310G>T

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

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

The ENST00000381639.3(RP9P):​n.308-310G>T variant causes a intron 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 ENST00000381639.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.855
• Publications: 1 publications found

Genes affected

RP9P (HGNC:):

RP9P (HGNC:33969): (RP9 pseudogene)

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000381639.3. 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
	RP9P	NR_003500.2		n.340-310G>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RP9P	ENST00000381639.3	TSL:1	n.308-310G>T		intron	N/A
	RP9P	ENST00000450133.5	TSL:6	n.170-4098G>T		intron	N/A
	RP9P	ENST00000685019.1		n.233-4098G>T		intron	N/A

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

African (AFR) AF: 0.118 AC: 4906 AN: 41406

American (AMR) AF: 0.129 AC: 1968 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.204 AC: 705 AN: 3464

East Asian (EAS) AF: 0.0588 AC: 301 AN: 5118

South Asian (SAS) AF: 0.184 AC: 884 AN: 4800

European-Finnish (FIN) AF: 0.117 AC: 1228 AN: 10538

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.170 AC: 11555 AN: 67958

Other (OTH) AF: 0.176 AC: 371 AN: 2108

Alfa AF: 0.160 Hom.: 5723

Bravo AF: 0.141

Asia WGS AF: 0.134 AC: 467 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.88
DANN	Benign	0.42
PhyloP100		-0.85
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs6945242; hg19: chr7-32973818;