chr13-64791868-T-G

Variant names:

• chr13-64791868-T-G
• rs9540221
• ENST00000739594.1:n.111-4315T>G

Variant summary

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

The ENST00000739594.1(ENSG00000296422):​n.111-4315T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.518 in 151,968 control chromosomes in the GnomAD database, including 22,558 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 0.52 (22558 hom., cov: 32)
• Consequence: ENSG00000296422 ENST00000739594.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.46
• Publications: 3 publications found

Genes affected

ENSG00000296422 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.738 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370240	XR_942030.1	n.117-4315T>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000296422	ENST00000739594.1	n.111-4315T>G		intron_variant	Intron 1 of 2
ENSG00000296422	ENST00000739595.1	n.122-4315T>G		intron_variant	Intron 1 of 2
ENSG00000296422	ENST00000739596.1	n.90-4315T>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.519 AC: 78783 AN: 151850 Hom.: 22568 Cov.: 32

Gnomad AFR AF: 0.266

Gnomad AMI AF: 0.558

Gnomad AMR AF: 0.544

Gnomad ASJ AF: 0.736

Gnomad EAS AF: 0.758

Gnomad SAS AF: 0.585

Gnomad FIN AF: 0.655

Gnomad MID AF: 0.586

Gnomad NFE AF: 0.610

Gnomad OTH AF: 0.563

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

GnomAD4 genome AF: 0.518 AC: 78794 AN: 151968 Hom.: 22558 Cov.: 32 AF XY: 0.522 AC XY: 38792 AN XY: 74252

African (AFR) AF: 0.265 AC: 11010 AN: 41490

American (AMR) AF: 0.544 AC: 8293 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.736 AC: 2557 AN: 3472

East Asian (EAS) AF: 0.758 AC: 3888 AN: 5132

South Asian (SAS) AF: 0.585 AC: 2815 AN: 4814

European-Finnish (FIN) AF: 0.655 AC: 6922 AN: 10568

Middle Eastern (MID) AF: 0.589 AC: 172 AN: 292

European-Non Finnish (NFE) AF: 0.610 AC: 41442 AN: 67924

Other (OTH) AF: 0.561 AC: 1188 AN: 2116

Alfa AF: 0.588 Hom.: 45633

Bravo AF: 0.498

Asia WGS AF: 0.648 AC: 2251 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	11
DANN	Benign	0.79
PhyloP100		1.5

Splicing

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

Other links and lift over

dbSNP: rs9540221; hg19: chr13-65366000; COSMIC: COSV69358303;