rs10497112

Variant names:

• chr2-152716561-T-C
• rs10497112
• NM_001365597.4:c.211-435A>G

Variant summary

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

The NM_001365597.4(PRPF40A):​c.211-435A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0323 in 152,296 control chromosomes in the GnomAD database, including 151 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 0.032 (151 hom., cov: 33)
• Consequence: PRPF40A NM_001365597.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0980

Genes affected

PRPF40A (HGNC:16463): (pre-mRNA processing factor 40 homolog A) Enables RNA binding activity. Involved in several processes, including cytoskeleton organization; regulation of cell shape; and regulation of cytokinesis. Located in nuclear matrix and nuclear speck. [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 (AFR) allele frequency at 95% confidence interval = 0.0784 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PRPF40A	NM_001365597.4	c.211-435A>G		intron_variant	Intron 1 of 25	ENST00000545856.8	NP_001352526.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PRPF40A	ENST00000545856.8	c.211-435A>G		intron_variant	Intron 1 of 25	1	NM_001365597.4	ENSP00000444656.4

Frequencies

GnomAD3 genomes AF: 0.0323 AC: 4916 AN: 152180 Hom.: 150 Cov.: 33

Gnomad AFR AF: 0.0807

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00910

Gnomad ASJ AF: 0.00490

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00435

Gnomad FIN AF: 0.0439

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0128

Gnomad OTH AF: 0.0229

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

GnomAD4 genome AF: 0.0323 AC: 4925 AN: 152296 Hom.: 151 Cov.: 33 AF XY: 0.0327 AC XY: 2437 AN XY: 74478

Gnomad4 AFR AF: 0.0807 AC: 0.0806941 AN: 0.0806941

Gnomad4 AMR AF: 0.00909 AC: 0.00908734 AN: 0.00908734

Gnomad4 ASJ AF: 0.00490 AC: 0.00489631 AN: 0.00489631

Gnomad4 EAS AF: 0.00 AC: 0 AN: 0

Gnomad4 SAS AF: 0.00394 AC: 0.00393701 AN: 0.00393701

Gnomad4 FIN AF: 0.0439 AC: 0.0439043 AN: 0.0439043

Gnomad4 NFE AF: 0.0128 AC: 0.0127889 AN: 0.0127889

Gnomad4 OTH AF: 0.0227 AC: 0.0227058 AN: 0.0227058

Alfa AF: 0.0173 Hom.: 97

Bravo AF: 0.0326

Asia WGS AF: 0.00664 AC: 24 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.1
DANN	Benign	0.62
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

Publications

LitVar

Other links and lift over

dbSNP: rs10497112; hg19: chr2-153573075;