rs2838769

Variant names:

• chr21-45072355-G-A
• rs2838769
• ENST00000599569.2:n.857C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 19 publications found

Genes affected

SSR4P1 (HGNC:):

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_027292.2. 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
	SSR4P1	NR_027292.2		n.857C>T		non_coding_transcript_exon	Exon 1 of 1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SSR4P1	ENST00000599569.2	TSL:6	n.857C>T		non_coding_transcript_exon	Exon 1 of 1
	SSR4P1	ENST00000429427.1	TSL:5	n.377-32C>T		intron	N/A
	SSR4P1	ENST00000734841.1		n.976-32C>T		intron	N/A

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

African (AFR) AF: 0.500 AC: 1 AN: 2

American (AMR) AF: 0.250 AC: 1 AN: 4

Ashkenazi Jewish (ASJ) AF: 0.500 AC: 1 AN: 2

East Asian (EAS) AF: 0.750 AC: 3 AN: 4

South Asian (SAS) AF: 0.500 AC: 1 AN: 2

European-Finnish (FIN) AF: 0.287 AC: 1782 AN: 6200

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.222 AC: 28 AN: 126

Other (OTH) AF: 0.271 AC: 13 AN: 48

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

African (AFR) AF: 0.192 AC: 7959 AN: 41528

American (AMR) AF: 0.161 AC: 2456 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.125 AC: 433 AN: 3472

East Asian (EAS) AF: 0.399 AC: 2061 AN: 5160

South Asian (SAS) AF: 0.221 AC: 1066 AN: 4830

European-Finnish (FIN) AF: 0.290 AC: 3074 AN: 10588

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.182 AC: 12373 AN: 68004

Other (OTH) AF: 0.187 AC: 396 AN: 2116

Alfa AF: 0.181 Hom.: 6913

Bravo AF: 0.190

Asia WGS AF: 0.310 AC: 1077 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.6
DANN	Benign	0.52
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs2838769; hg19: chr21-46492270;