13-37289072-T-C

Variant names:

• chr13-37289072-T-C
• rs1924449
• ENST00000827668.1:n.233-18280T>C

Variant summary

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

The ENST00000827668.1(ENSG00000307651):​n.233-18280T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.903 in 152,120 control chromosomes in the GnomAD database, including 63,327 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 0.90 (63327 hom., cov: 31)
• Consequence: ENSG00000307651 ENST00000827668.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.29
• Publications: 1 publications found

Genes affected

ENSG00000307651 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.981 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
ENSG00000307651	ENST00000827668.1	n.233-18280T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.903 AC: 137228 AN: 152002 Hom.: 63303 Cov.: 31

Gnomad AFR AF: 0.689

Gnomad AMI AF: 0.939

Gnomad AMR AF: 0.955

Gnomad ASJ AF: 0.994

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.986

Gnomad FIN AF: 0.996

Gnomad MID AF: 0.975

Gnomad NFE AF: 0.987

Gnomad OTH AF: 0.930

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

GnomAD4 genome AF: 0.903 AC: 137301 AN: 152120 Hom.: 63327 Cov.: 31 AF XY: 0.906 AC XY: 67406 AN XY: 74402

African (AFR) AF: 0.689 AC: 28554 AN: 41456

American (AMR) AF: 0.955 AC: 14576 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.994 AC: 3448 AN: 3470

East Asian (EAS) AF: 1.00 AC: 5176 AN: 5176

South Asian (SAS) AF: 0.986 AC: 4767 AN: 4834

European-Finnish (FIN) AF: 0.996 AC: 10568 AN: 10614

Middle Eastern (MID) AF: 0.976 AC: 287 AN: 294

European-Non Finnish (NFE) AF: 0.987 AC: 67105 AN: 67996

Other (OTH) AF: 0.931 AC: 1964 AN: 2110

Alfa AF: 0.925 Hom.: 4796

Bravo AF: 0.890

Asia WGS AF: 0.973 AC: 3380 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	8.2
DANN	Benign	0.77
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs1924449; hg19: chr13-37863209;