chr5-121982225-C-T

Variant names:

• chr5-121982225-C-T
• rs4496732
• NM_152546.3:c.198+6838C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_152546.3(SRFBP1):​c.198+6838C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.883 in 151,916 control chromosomes in the GnomAD database, including 59,270 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 0.88 (59270 hom., cov: 31)
• Consequence: SRFBP1 NM_152546.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.700
• Publications: 4 publications found

Genes affected

SRFBP1 (HGNC:26333): (serum response factor binding protein 1) Enables RNA binding activity. Predicted to be involved in maturation of SSU-rRNA. Predicted to be located in perinuclear region of cytoplasm. Predicted to be part of 90S preribosome. Predicted to be active in nucleus. [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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.941 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SRFBP1	NM_152546.3	c.198+6838C>T		intron_variant	Intron 3 of 7	ENST00000339397.5	NP_689759.2
SRFBP1	XM_017009111.3	c.198+6838C>T		intron_variant	Intron 3 of 7		XP_016864600.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SRFBP1	ENST00000339397.5	c.198+6838C>T		intron_variant	Intron 3 of 7	1	NM_152546.3	ENSP00000341324.4

Frequencies

GnomAD3 genomes AF: 0.883 AC: 133990 AN: 151798 Hom.: 59222 Cov.: 31

Gnomad AFR AF: 0.909

Gnomad AMI AF: 0.978

Gnomad AMR AF: 0.885

Gnomad ASJ AF: 0.852

Gnomad EAS AF: 0.964

Gnomad SAS AF: 0.866

Gnomad FIN AF: 0.887

Gnomad MID AF: 0.911

Gnomad NFE AF: 0.861

Gnomad OTH AF: 0.867

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

GnomAD4 genome AF: 0.883 AC: 134097 AN: 151916 Hom.: 59270 Cov.: 31 AF XY: 0.884 AC XY: 65679 AN XY: 74274

African (AFR) AF: 0.909 AC: 37713 AN: 41486

American (AMR) AF: 0.886 AC: 13490 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.852 AC: 2953 AN: 3464

East Asian (EAS) AF: 0.963 AC: 4989 AN: 5180

South Asian (SAS) AF: 0.867 AC: 4182 AN: 4824

European-Finnish (FIN) AF: 0.887 AC: 9395 AN: 10596

Middle Eastern (MID) AF: 0.901 AC: 265 AN: 294

European-Non Finnish (NFE) AF: 0.861 AC: 58390 AN: 67826

Other (OTH) AF: 0.869 AC: 1828 AN: 2104

Alfa AF: 0.868 Hom.: 8319

Bravo AF: 0.886

Asia WGS AF: 0.927 AC: 3222 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.3
DANN	Benign	0.49
PhyloP100		0.70
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: rs4496732; hg19: chr5-121317920;