rs618687

Positions:

• chr10-42736971-A-G

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

RSU1P1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RSU1P1		n.42736971A>G		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RSU1P1	ENST00000453416.1	n.324-71A>G		intron_variant		6

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

Gnomad4 AFR exome AF: 0.379

Gnomad4 AMR exome AF: 0.241

Gnomad4 ASJ exome AF: 0.139

Gnomad4 EAS exome AF: 0.242

Gnomad4 SAS exome AF: 0.180

Gnomad4 FIN exome AF: 0.129

Gnomad4 NFE exome AF: 0.132

Gnomad4 OTH exome AF: 0.171

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

Gnomad4 AFR AF: 0.372

Gnomad4 AMR AF: 0.212

Gnomad4 ASJ AF: 0.137

Gnomad4 EAS AF: 0.303

Gnomad4 SAS AF: 0.194

Gnomad4 FIN AF: 0.128

Gnomad4 NFE AF: 0.137

Gnomad4 OTH AF: 0.206

Alfa AF: 0.179 Hom.: 383

Bravo AF: 0.231

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs618687; hg19: chr10-43232419;