13-37290661-G-T

Variant names:

• chr13-37290661-G-T
• rs9547776
• ENST00000827668.1:n.233-16691G>T

Variant summary

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

The ENST00000827668.1(ENSG00000307651):​n.233-16691G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.902 in 152,060 control chromosomes in the GnomAD database, including 63,246 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 (63246 hom., cov: 30)
• Consequence: ENSG00000307651 ENST00000827668.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.171
• Publications: 2 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=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.981 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000827668.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000307651	ENST00000827668.1		n.233-16691G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.902 AC: 137121 AN: 151942 Hom.: 63222 Cov.: 30

Gnomad AFR AF: 0.689

Gnomad AMI AF: 0.938

Gnomad AMR AF: 0.955

Gnomad ASJ AF: 0.994

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.973

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: 0.902 AC: 137194 AN: 152060 Hom.: 63246 Cov.: 30 AF XY: 0.905 AC XY: 67327 AN XY: 74364

African (AFR) AF: 0.689 AC: 28573 AN: 41456

American (AMR) AF: 0.955 AC: 14578 AN: 15264

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

East Asian (EAS) AF: 1.00 AC: 5154 AN: 5154

South Asian (SAS) AF: 0.973 AC: 4683 AN: 4814

European-Finnish (FIN) AF: 0.996 AC: 10574 AN: 10620

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

European-Non Finnish (NFE) AF: 0.987 AC: 67079 AN: 67968

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

Alfa AF: 0.928 Hom.: 3617

Bravo AF: 0.890

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.6
DANN	Benign	0.45
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs9547776; hg19: chr13-37864798;