13-39997916-G-A

Variant names:

• chr13-39997916-G-A
• rs7339164
• ENST00000837163.1:n.601C>T

Variant summary

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

The ENST00000837163.1(ENSG00000308901):​n.601C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.299 in 151,980 control chromosomes in the GnomAD database, including 7,533 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 0.30 (7533 hom., cov: 32)
• Consequence: ENSG00000308901 ENST00000837163.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.222
• Publications: 3 publications found

Genes affected

ENSG00000308901 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.382 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000837163.1. 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
	ENSG00000308901	ENST00000837163.1		n.601C>T		non_coding_transcript_exon	Exon 4 of 4

Frequencies

GnomAD3 genomes AF: 0.300 AC: 45487 AN: 151862 Hom.: 7531 Cov.: 32

Gnomad AFR AF: 0.162

Gnomad AMI AF: 0.377

Gnomad AMR AF: 0.390

Gnomad ASJ AF: 0.283

Gnomad EAS AF: 0.170

Gnomad SAS AF: 0.229

Gnomad FIN AF: 0.356

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.369

Gnomad OTH AF: 0.296

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

GnomAD4 genome AF: 0.299 AC: 45500 AN: 151980 Hom.: 7533 Cov.: 32 AF XY: 0.297 AC XY: 22091 AN XY: 74286

African (AFR) AF: 0.162 AC: 6719 AN: 41462

American (AMR) AF: 0.390 AC: 5959 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.283 AC: 982 AN: 3468

East Asian (EAS) AF: 0.170 AC: 879 AN: 5168

South Asian (SAS) AF: 0.228 AC: 1096 AN: 4812

European-Finnish (FIN) AF: 0.356 AC: 3752 AN: 10528

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.369 AC: 25085 AN: 67962

Other (OTH) AF: 0.292 AC: 616 AN: 2110

Alfa AF: 0.348 Hom.: 5532

Bravo AF: 0.299

Asia WGS AF: 0.189 AC: 658 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.1
DANN	Benign	0.53
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs7339164; hg19: chr13-40572053; COSMIC: COSV69954097;