rs4773396

Positions:

• chr13-111589370-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000375713.1(ENSG00000204398):​n.54+1026G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.438 in 152,048 control chromosomes in the GnomAD database, including 16,005 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 0.44 (15996 hom., cov: 32)
  • Exomes 𝑓: 0.52 (9 hom.)
• Consequence: ENST00000375713.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0340

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.521 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000375713.1	n.54+1026G>A		intron_variant, non_coding_transcript_variant		5
	ENST00000607406.1	n.1170G>A		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.438 AC: 66459 AN: 151876 Hom.: 15976 Cov.: 32

Gnomad AFR AF: 0.220

Gnomad AMI AF: 0.576

Gnomad AMR AF: 0.468

Gnomad ASJ AF: 0.458

Gnomad EAS AF: 0.530

Gnomad SAS AF: 0.429

Gnomad FIN AF: 0.613

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.526

Gnomad OTH AF: 0.448

GnomAD4 exome AF: 0.518 AC: 29 AN: 56 Hom.: 9 Cov.: 0 AF XY: 0.565 AC XY: 26 AN XY: 46

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 NFE exome AF: 0.568

Gnomad4 OTH exome AF: 0.333

GnomAD4 genome AF: 0.438 AC: 66510 AN: 151992 Hom.: 15996 Cov.: 32 AF XY: 0.442 AC XY: 32847 AN XY: 74298

Gnomad4 AFR AF: 0.220

Gnomad4 AMR AF: 0.469

Gnomad4 ASJ AF: 0.458

Gnomad4 EAS AF: 0.531

Gnomad4 SAS AF: 0.431

Gnomad4 FIN AF: 0.613

Gnomad4 NFE AF: 0.526

Gnomad4 OTH AF: 0.449

Alfa AF: 0.472 Hom.: 3006

Bravo AF: 0.420

Asia WGS AF: 0.458 AC: 1592 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	4.4
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4773396; hg19: chr13-112241717;