13-81209054-C-T

Variant names:

• chr13-81209054-C-T
• rs7321904
• ENST00000728555.1:n.221-8619C>T

Variant summary

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

The ENST00000728555.1(ENSG00000295193):​n.221-8619C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.126 in 152,140 control chromosomes in the GnomAD database, including 1,493 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 0.13 (1493 hom., cov: 32)
• Consequence: ENSG00000295193 ENST00000728555.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.80
• Publications: 2 publications found

Genes affected

ENSG00000295193 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.284 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
ENSG00000295193	ENST00000728555.1	n.221-8619C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.126 AC: 19126 AN: 152022 Hom.: 1489 Cov.: 32

Gnomad AFR AF: 0.192

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.109

Gnomad ASJ AF: 0.110

Gnomad EAS AF: 0.296

Gnomad SAS AF: 0.153

Gnomad FIN AF: 0.0913

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.0815

Gnomad OTH AF: 0.136

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

GnomAD4 genome AF: 0.126 AC: 19165 AN: 152140 Hom.: 1493 Cov.: 32 AF XY: 0.128 AC XY: 9511 AN XY: 74394

African (AFR) AF: 0.192 AC: 7965 AN: 41474

American (AMR) AF: 0.109 AC: 1674 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.110 AC: 383 AN: 3472

East Asian (EAS) AF: 0.297 AC: 1532 AN: 5164

South Asian (SAS) AF: 0.154 AC: 740 AN: 4820

European-Finnish (FIN) AF: 0.0913 AC: 967 AN: 10592

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.0816 AC: 5547 AN: 68000

Other (OTH) AF: 0.141 AC: 298 AN: 2112

Alfa AF: 0.101 Hom.: 1802

Bravo AF: 0.129

Asia WGS AF: 0.243 AC: 844 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.071
DANN	Benign	0.48
PhyloP100		-2.8

Splicing

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

Other links and lift over

dbSNP: rs7321904; hg19: chr13-81783189; COSMIC: COSV69017272;