rs34315612

Positions:

• chr19-49033309-T-C

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_Strong BS2

The ENST00000604577.1(ENSG00000267335):​c.9+3394A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0051 in 1,606,264 control chromosomes in the GnomAD database, including 55 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 0.0038 (1 hom., cov: 30)
  • Exomes 𝑓: 0.0052 (54 hom.)
• Consequence: ENSG00000267335 ENST00000604577.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.805

Genes affected

ENSG00000267335 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BS2: High Homozygotes in GnomAdExome4 at 54 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.49033309T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000267335	ENST00000591656.1	c.-28+3217A>G		intron_variant		2		ENSP00000466140.1
ENSG00000267335	ENST00000604577.1	c.9+3394A>G		intron_variant		1		ENSP00000474022.1

Frequencies

GnomAD3 genomes AF: 0.00380 AC: 577 AN: 151892 Hom.: 1 Cov.: 30

Gnomad AFR AF: 0.000970

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00203

Gnomad ASJ AF: 0.00346

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.00415

Gnomad FIN AF: 0.00905

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.00547

Gnomad OTH AF: 0.00144

GnomAD4 exome AF: 0.00524 AC: 7620 AN: 1454254 Hom.: 54 AF XY: 0.00527 AC XY: 3809 AN XY: 723004

Gnomad4 AFR exome AF: 0.000723

Gnomad4 AMR exome AF: 0.00341

Gnomad4 ASJ exome AF: 0.00237

Gnomad4 EAS exome AF: 0.0000757

Gnomad4 SAS exome AF: 0.00689

Gnomad4 FIN exome AF: 0.00779

Gnomad4 NFE exome AF: 0.00546

Gnomad4 OTH exome AF: 0.00522

GnomAD4 genome AF: 0.00379 AC: 576 AN: 152010 Hom.: 1 Cov.: 30 AF XY: 0.00390 AC XY: 290 AN XY: 74296

Gnomad4 AFR AF: 0.000967

Gnomad4 AMR AF: 0.00203

Gnomad4 ASJ AF: 0.00346

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.00395

Gnomad4 FIN AF: 0.00905

Gnomad4 NFE AF: 0.00547

Gnomad4 OTH AF: 0.00142

Alfa AF: 0.00376 Hom.: 0

Bravo AF: 0.00321

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	16
DANN	Benign	0.28

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: rs34315612; hg19: chr19-49536566;