13-53389022-T-C

Variant names:

• chr13-53389022-T-C
• rs964028
• ENST00000615176.1:n.749-1404T>C

Variant summary

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

The ENST00000615176.1(ENSG00000273919):​n.749-1404T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.937 in 152,148 control chromosomes in the GnomAD database, including 67,340 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 0.94 (67340 hom., cov: 31)
• Consequence: ENSG00000273919 ENST00000615176.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0640

Genes affected

ENSG00000273919 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.992 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
ENSG00000273919	ENST00000615176.1	n.749-1404T>C		intron_variant	Intron 1 of 2	2
ENSG00000287722	ENST00000657016.1	n.629+84900T>C		intron_variant	Intron 2 of 3
ENSG00000288768	ENST00000688155.1	n.45+24617T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.937 AC: 142393 AN: 152030 Hom.: 67297 Cov.: 31

Gnomad AFR AF: 0.786

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.970

Gnomad ASJ AF: 0.978

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.999

Gnomad FIN AF: 0.996

Gnomad MID AF: 0.984

Gnomad NFE AF: 0.998

Gnomad OTH AF: 0.955

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

GnomAD4 genome AF: 0.937 AC: 142493 AN: 152148 Hom.: 67340 Cov.: 31 AF XY: 0.939 AC XY: 69829 AN XY: 74376

Gnomad4 AFR AF: 0.787

Gnomad4 AMR AF: 0.970

Gnomad4 ASJ AF: 0.978

Gnomad4 EAS AF: 1.00

Gnomad4 SAS AF: 0.999

Gnomad4 FIN AF: 0.996

Gnomad4 NFE AF: 0.998

Gnomad4 OTH AF: 0.955

Alfa AF: 0.959 Hom.: 10363

Bravo AF: 0.929

Asia WGS AF: 0.988 AC: 3430 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.1
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs964028; hg19: chr13-53963157;