rs2838769

chr21-45072355-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_027292.2(SSR4P1):n.857C>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 0.202 in 158,594 control chromosomes in the GnomAD database, including 3,465 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 0.20 (3190 hom., cov: 33)
  • Exomes 𝑓: 0.29 (275 hom.)
• Consequence: SSR4P1 NR_027292.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.412

Genes affected

SSR4P1 (HGNC:23131): (signal sequence receptor subunit 4 pseudogene 1)

LOC105372836 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.385 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SSR4P1	NR_027292.2	n.857C>T		non_coding_transcript_exon_variant	1/1
LOC105372836	XR_937796.3	n.269+1118C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SSR4P1	ENST00000429427.1	n.377-32C>T		intron_variant, non_coding_transcript_variant		5
SSR4P1	ENST00000599569.2	n.857C>T		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.198 AC: 30156 AN: 152088 Hom.: 3193 Cov.: 33

Gnomad AFR AF: 0.192

Gnomad AMI AF: 0.330

Gnomad AMR AF: 0.161

Gnomad ASJ AF: 0.125

Gnomad EAS AF: 0.400

Gnomad SAS AF: 0.221

Gnomad FIN AF: 0.290

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.182

Gnomad OTH AF: 0.190

GnomAD4 exome AF: 0.286 AC: 1830 AN: 6388 Hom.: 275 Cov.: 0 AF XY: 0.287 AC XY: 898 AN XY: 3130

Gnomad4 AFR exome AF: 0.500

Gnomad4 AMR exome AF: 0.250

Gnomad4 ASJ exome AF: 0.500

Gnomad4 EAS exome AF: 0.750

Gnomad4 SAS exome AF: 0.500

Gnomad4 FIN exome AF: 0.287

Gnomad4 NFE exome AF: 0.222

Gnomad4 OTH exome AF: 0.271

GnomAD4 genome AF: 0.198 AC: 30155 AN: 152206 Hom.: 3190 Cov.: 33 AF XY: 0.204 AC XY: 15202 AN XY: 74404

Gnomad4 AFR AF: 0.192

Gnomad4 AMR AF: 0.161

Gnomad4 ASJ AF: 0.125

Gnomad4 EAS AF: 0.399

Gnomad4 SAS AF: 0.221

Gnomad4 FIN AF: 0.290

Gnomad4 NFE AF: 0.182

Gnomad4 OTH AF: 0.187

Alfa AF: 0.177 Hom.: 3854

Bravo AF: 0.190

Asia WGS AF: 0.310 AC: 1077 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	1.6
Dann	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2838769; hg19: chr21-46492270;