rs17431357

Variant names:

• chr12-120442631-C-T
• rs17431357
• ENST00000551806.1:c.175-4026C>T

Variant summary

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

The ENST00000551806.1(ENSG00000111780):​c.175-4026C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0453 in 152,296 control chromosomes in the GnomAD database, including 262 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 0.045 (262 hom., cov: 31)
• Consequence: ENSG00000111780 ENST00000551806.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.551
• Publications: 18 publications found

Genes affected

ENSG00000111780 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0922 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000111780	ENST00000551806.1	c.175-4026C>T		intron_variant	Intron 2 of 4	3		ENSP00000450281.1

Frequencies

GnomAD3 genomes AF: 0.0454 AC: 6911 AN: 152178 Hom.: 264 Cov.: 31

Gnomad AFR AF: 0.0102

Gnomad AMI AF: 0.0362

Gnomad AMR AF: 0.0385

Gnomad ASJ AF: 0.0573

Gnomad EAS AF: 0.00347

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.0940

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0595

Gnomad OTH AF: 0.0449

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

GnomAD4 genome AF: 0.0453 AC: 6903 AN: 152296 Hom.: 262 Cov.: 31 AF XY: 0.0473 AC XY: 3521 AN XY: 74464

African (AFR) AF: 0.0102 AC: 424 AN: 41562

American (AMR) AF: 0.0385 AC: 588 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0573 AC: 199 AN: 3470

East Asian (EAS) AF: 0.00347 AC: 18 AN: 5182

South Asian (SAS) AF: 0.0995 AC: 480 AN: 4824

European-Finnish (FIN) AF: 0.0940 AC: 998 AN: 10614

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0595 AC: 4051 AN: 68034

Other (OTH) AF: 0.0440 AC: 93 AN: 2116

Alfa AF: 0.0515 Hom.: 411

Bravo AF: 0.0373

Asia WGS AF: 0.0460 AC: 160 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.3
DANN	Benign	0.86
PhyloP100		0.55

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: rs17431357; hg19: chr12-120880434;