rs11884064

Variant names:

• chr2-45609914-T-C
• rs11884064
• NM_018079.5:c.-1+1305A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 8 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
SRBD1	NM_018079.5	c.-1+1305A>G		intron_variant	Intron 1 of 20	ENST00000263736.5	NP_060549.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SRBD1	ENST00000263736.5	c.-1+1305A>G		intron_variant	Intron 1 of 20	2	NM_018079.5	ENSP00000263736.4
SRBD1	ENST00000461805.1	n.313+1305A>G		intron_variant	Intron 2 of 3	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

African (AFR) AF: 0.116 AC: 4807 AN: 41526

American (AMR) AF: 0.209 AC: 3190 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.255 AC: 885 AN: 3470

East Asian (EAS) AF: 0.277 AC: 1439 AN: 5190

South Asian (SAS) AF: 0.237 AC: 1145 AN: 4824

European-Finnish (FIN) AF: 0.164 AC: 1732 AN: 10580

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.229 AC: 15604 AN: 68016

Other (OTH) AF: 0.196 AC: 413 AN: 2106

Alfa AF: 0.218 Hom.: 10034

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
PhyloP100		-0.68
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs11884064; hg19: chr2-45837053;