rs11243426

Variant names:

• chr9-131558975-C-T
• rs11243426
• NM_001395643.1:c.*773C>T

Variant summary

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

The NM_001395643.1(PRRT1B):​c.*773C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.232 in 152,108 control chromosomes in the GnomAD database, including 4,732 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 0.23 (4732 hom., cov: 33)
• Consequence: PRRT1B NM_001395643.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.59
• Publications: 0 publications found

Genes affected

PRRT1B (HGNC:53642): (proline rich transmembrane protein 1B) Predicted to be integral component of membrane. Predicted to be active in membrane. [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=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.474 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PRRT1B	NM_001395643.1	c.*773C>T		3_prime_UTR_variant	Exon 4 of 4	ENST00000636672.2	NP_001382572.1
PRRT1B	NM_001365666.1	c.*773C>T		3_prime_UTR_variant	Exon 4 of 4		NP_001352595.1
PRRT1B	XM_017015412.3	c.*773C>T		3_prime_UTR_variant	Exon 3 of 3		XP_016870901.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PRRT1B	ENST00000636672.2	c.*773C>T		3_prime_UTR_variant	Exon 4 of 4	5	NM_001395643.1	ENSP00000490857.1
PRRT1B	ENST00000850862.1	n.*1583C>T		non_coding_transcript_exon_variant	Exon 5 of 5			ENSP00000520949.1
PRRT1B	ENST00000850862.1	n.*1583C>T		3_prime_UTR_variant	Exon 5 of 5			ENSP00000520949.1

Frequencies

GnomAD3 genomes AF: 0.232 AC: 35228 AN: 151988 Hom.: 4731 Cov.: 33

Gnomad AFR AF: 0.116

Gnomad AMI AF: 0.238

Gnomad AMR AF: 0.349

Gnomad ASJ AF: 0.332

Gnomad EAS AF: 0.489

Gnomad SAS AF: 0.246

Gnomad FIN AF: 0.215

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.252

Gnomad OTH AF: 0.252

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

GnomAD4 genome AF: 0.232 AC: 35230 AN: 152108 Hom.: 4732 Cov.: 33 AF XY: 0.233 AC XY: 17363 AN XY: 74360

African (AFR) AF: 0.115 AC: 4792 AN: 41516

American (AMR) AF: 0.349 AC: 5324 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.332 AC: 1152 AN: 3472

East Asian (EAS) AF: 0.490 AC: 2531 AN: 5168

South Asian (SAS) AF: 0.247 AC: 1187 AN: 4814

European-Finnish (FIN) AF: 0.215 AC: 2278 AN: 10580

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.252 AC: 17116 AN: 67972

Other (OTH) AF: 0.250 AC: 529 AN: 2112

Alfa AF: 0.258 Hom.: 9966

Bravo AF: 0.240

Asia WGS AF: 0.340 AC: 1181 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.19
DANN	Benign	0.63
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs11243426; hg19: chr9-134434362; COSMIC: COSV60404168;