17-44364976-T-C

Variant names:

• chr17-44364976-T-C
• rs708382

Variant summary

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

The variant allele was found at a frequency of 0.393 in 692,192 control chromosomes in the GnomAD database, including 54,036 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 0.39 (11891 hom., cov: 31)
  • Exomes 𝑓: 0.39 (42145 hom.)
• Consequence: RPL7L1P5 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.226
• Publications: 36 publications found

Genes affected

RPL7L1P5 (HGNC:39487): (RPL7L1 pseudogene 5)

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 (EAS) allele frequency at 95% confidence interval = 0.431 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000590816.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RPL7L1P5	ENST00000590816.1	TSL:6	n.*38A>G		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.395 AC: 59975 AN: 151752 Hom.: 11896 Cov.: 31

Gnomad AFR AF: 0.391

Gnomad AMI AF: 0.413

Gnomad AMR AF: 0.360

Gnomad ASJ AF: 0.450

Gnomad EAS AF: 0.447

Gnomad SAS AF: 0.355

Gnomad FIN AF: 0.439

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.396

Gnomad OTH AF: 0.370

GnomAD4 exome AF: 0.392 AC: 212054 AN: 540322 Hom.: 42145 Cov.: 6 AF XY: 0.390 AC XY: 113019 AN XY: 289802

African (AFR) AF: 0.380 AC: 5565 AN: 14664

American (AMR) AF: 0.389 AC: 10923 AN: 28100

Ashkenazi Jewish (ASJ) AF: 0.440 AC: 8113 AN: 18418

East Asian (EAS) AF: 0.432 AC: 13329 AN: 30870

South Asian (SAS) AF: 0.351 AC: 20707 AN: 59000

European-Finnish (FIN) AF: 0.435 AC: 13614 AN: 31294

Middle Eastern (MID) AF: 0.346 AC: 797 AN: 2302

European-Non Finnish (NFE) AF: 0.391 AC: 127616 AN: 326514

Other (OTH) AF: 0.391 AC: 11390 AN: 29160

GnomAD4 genome AF: 0.395 AC: 59981 AN: 151870 Hom.: 11891 Cov.: 31 AF XY: 0.393 AC XY: 29134 AN XY: 74188

African (AFR) AF: 0.390 AC: 16170 AN: 41414

American (AMR) AF: 0.360 AC: 5489 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.450 AC: 1560 AN: 3468

East Asian (EAS) AF: 0.446 AC: 2310 AN: 5174

South Asian (SAS) AF: 0.353 AC: 1699 AN: 4812

European-Finnish (FIN) AF: 0.439 AC: 4610 AN: 10512

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.396 AC: 26900 AN: 67924

Other (OTH) AF: 0.367 AC: 772 AN: 2104

Alfa AF: 0.393 Hom.: 48045

Bravo AF: 0.389

Asia WGS AF: 0.405 AC: 1416 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	5.3
DANN	Benign	0.59
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs708382; hg19: chr17-42442344;