rs618687

Variant names:

• chr10-42736971-A-G
• rs618687

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 0.172 in 665,406 control chromosomes in the GnomAD database, including 11,792 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 0.22 (4415 hom., cov: 32)
  • Exomes 𝑓: 0.16 (7377 hom.)
• Consequence: RSU1P1 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.98
• Publications: 2 publications found

Genes affected

RSU1P1 (HGNC:31114): (Ras suppressor protein 1 pseudogene 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.367 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000453416.1. 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
	RSU1P1	ENST00000453416.1	TSL:6	n.324-71A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.216 AC: 32884 AN: 151960 Hom.: 4390 Cov.: 32

Gnomad AFR AF: 0.371

Gnomad AMI AF: 0.205

Gnomad AMR AF: 0.212

Gnomad ASJ AF: 0.137

Gnomad EAS AF: 0.304

Gnomad SAS AF: 0.196

Gnomad FIN AF: 0.128

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.137

Gnomad OTH AF: 0.206

GnomAD4 exome AF: 0.158 AC: 81281 AN: 513328 Hom.: 7377 Cov.: 5 AF XY: 0.157 AC XY: 43243 AN XY: 276176

African (AFR) AF: 0.379 AC: 5380 AN: 14188

American (AMR) AF: 0.241 AC: 6443 AN: 26714

Ashkenazi Jewish (ASJ) AF: 0.139 AC: 2058 AN: 14822

East Asian (EAS) AF: 0.242 AC: 7693 AN: 31762

South Asian (SAS) AF: 0.180 AC: 9386 AN: 52194

European-Finnish (FIN) AF: 0.129 AC: 5942 AN: 46062

Middle Eastern (MID) AF: 0.137 AC: 497 AN: 3624

European-Non Finnish (NFE) AF: 0.132 AC: 39136 AN: 296228

Other (OTH) AF: 0.171 AC: 4746 AN: 27734

GnomAD4 genome AF: 0.217 AC: 32950 AN: 152078 Hom.: 4415 Cov.: 32 AF XY: 0.216 AC XY: 16071 AN XY: 74346

African (AFR) AF: 0.372 AC: 15417 AN: 41452

American (AMR) AF: 0.212 AC: 3233 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.137 AC: 477 AN: 3472

East Asian (EAS) AF: 0.303 AC: 1562 AN: 5158

South Asian (SAS) AF: 0.194 AC: 937 AN: 4818

European-Finnish (FIN) AF: 0.128 AC: 1354 AN: 10606

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.137 AC: 9307 AN: 67976

Other (OTH) AF: 0.206 AC: 434 AN: 2108

Alfa AF: 0.179 Hom.: 383

Bravo AF: 0.231

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	10
DANN	Benign	0.33
PhyloP100		2.0

Splicing

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

Other links and lift over

dbSNP: rs618687; hg19: chr10-43232419;