rs11884064

Positions:

• chr2-45609914-T-C

Variant summary

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

The NM_018079.5(SRBD1):​c.-1+1305A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.194 in 152,210 control chromosomes in the GnomAD database, including 3,071 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 0.19 (3071 hom., cov: 32)
• Consequence: SRBD1 NM_018079.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.678

Genes affected

SRBD1 (HGNC:25521): (S1 RNA binding domain 1) Predicted to enable mRNA binding activity. Predicted to be a structural constituent of ribosome. Predicted to be involved in translation. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.265 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SRBD1	NM_018079.5	c.-1+1305A>G		intron_variant		ENST00000263736.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SRBD1	ENST00000263736.5	c.-1+1305A>G		intron_variant		2	NM_018079.5	P1
SRBD1	ENST00000461805.1	n.313+1305A>G		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.194 AC: 29493 AN: 152092 Hom.: 3070 Cov.: 32

Gnomad AFR AF: 0.116

Gnomad AMI AF: 0.229

Gnomad AMR AF: 0.209

Gnomad ASJ AF: 0.255

Gnomad EAS AF: 0.278

Gnomad SAS AF: 0.237

Gnomad FIN AF: 0.164

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.229

Gnomad OTH AF: 0.194

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.194 AC: 29504 AN: 152210 Hom.: 3071 Cov.: 32 AF XY: 0.195 AC XY: 14483 AN XY: 74410

Gnomad4 AFR AF: 0.116

Gnomad4 AMR AF: 0.209

Gnomad4 ASJ AF: 0.255

Gnomad4 EAS AF: 0.277

Gnomad4 SAS AF: 0.237

Gnomad4 FIN AF: 0.164

Gnomad4 NFE AF: 0.229

Gnomad4 OTH AF: 0.196

Alfa AF: 0.224 Hom.: 4098

Bravo AF: 0.193

Asia WGS AF: 0.245 AC: 853 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.2
DANN	Benign	0.41

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs11884064; hg19: chr2-45837053;