rs9588771

Variant names:

• chr13-89833675-G-A
• rs9588771
• ENST00000448259.1:n.267C>T

Your query was ambiguous. Multiple possible variants found:

• chr13-89833675-G-A
• chr13-89833675-G-C

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000448259.1(RPL7L1P1):​n.267C>T 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 0.000305 in 623,388 control chromosomes in the GnomAD database, including 1 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 0.00086 (0 hom., cov: 32)
  • Exomes 𝑓: 0.00013 (1 hom.)
• Consequence: RPL7L1P1 ENST00000448259.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.296
• Publications: 1 publications found

Genes affected

RPL7L1P1 (HGNC:39455): (RPL7L1 pseudogene 1)

LINC02336 (HGNC:53256): (long intergenic non-protein coding RNA 2336)

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RPL7L1P1		n.89833675G>A		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RPL7L1P1	ENST00000448259.1	n.267C>T		non_coding_transcript_exon_variant	Exon 1 of 1	6
LINC02336	ENST00000756840.1	n.871G>A		non_coding_transcript_exon_variant	Exon 5 of 5

Frequencies

GnomAD3 genomes AF: 0.000862 AC: 131 AN: 152024 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.00285

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000525

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000294

Gnomad OTH AF: 0.00143

GnomAD4 exome AF: 0.000125 AC: 59 AN: 471246 Hom.: 1 Cov.: 0 AF XY: 0.0000940 AC XY: 24 AN XY: 255380

African (AFR) AF: 0.00200 AC: 27 AN: 13524

American (AMR) AF: 0.0000777 AC: 2 AN: 25744

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 13946

East Asian (EAS) AF: 0.00 AC: 0 AN: 31154

South Asian (SAS) AF: 0.000149 AC: 8 AN: 53650

European-Finnish (FIN) AF: 0.0000349 AC: 1 AN: 28640

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1856

European-Non Finnish (NFE) AF: 0.0000325 AC: 9 AN: 276922

Other (OTH) AF: 0.000465 AC: 12 AN: 25810

GnomAD4 genome AF: 0.000861 AC: 131 AN: 152142 Hom.: 0 Cov.: 32 AF XY: 0.000861 AC XY: 64 AN XY: 74372

African (AFR) AF: 0.00284 AC: 118 AN: 41514

American (AMR) AF: 0.000524 AC: 8 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5170

South Asian (SAS) AF: 0.00 AC: 0 AN: 4818

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10590

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.0000294 AC: 2 AN: 68000

Other (OTH) AF: 0.00142 AC: 3 AN: 2114

Alfa AF: 0.000270 Hom.: 0

Bravo AF: 0.000763

Asia WGS AF: 0.000577 AC: 2 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.3
DANN	Benign	0.72
PhyloP100		-0.30

Splicing

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

Other links and lift over

dbSNP: rs9588771; hg19: chr13-90485929;