rs4773396

Variant names:

• chr13-111589370-G-A
• rs4773396
• ENST00000607406.1:n.1170G>A

Variant summary

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

The ENST00000607406.1(ENSG00000204398):​n.1170G>A variant causes a non coding transcript exon 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: ENSG00000204398 ENST00000607406.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0340

Genes affected

ENSG00000204398 (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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000204398	ENST00000607406.1	n.1170G>A		non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000204398	ENST00000375713.1	n.54+1026G>A		intron_variant	Intron 1 of 3	5

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;