ENST00000802609.1:n.68-4122C>T

Variant names:

• chr13-97551473-G-A
• rs349114
• ENST00000802609.1:n.68-4122C>T

Variant summary

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

The ENST00000802609.1(ENSG00000304344):​n.68-4122C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.165 in 152,058 control chromosomes in the GnomAD database, including 2,396 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 0.16 (2396 hom., cov: 32)
• Consequence: ENSG00000304344 ENST00000802609.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.181
• Publications: 9 publications found

Genes affected

ENSG00000304344 (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 (NFE) allele frequency at 95% confidence interval = 0.205 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000802609.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000304344	ENST00000802609.1		n.68-4122C>T		intron	N/A
	ENSG00000304344	ENST00000802610.1		n.135-4122C>T		intron	N/A
	ENSG00000304344	ENST00000802611.1		n.139-4122C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.165 AC: 25038 AN: 151940 Hom.: 2391 Cov.: 32

Gnomad AFR AF: 0.0802

Gnomad AMI AF: 0.0969

Gnomad AMR AF: 0.188

Gnomad ASJ AF: 0.0979

Gnomad EAS AF: 0.192

Gnomad SAS AF: 0.133

Gnomad FIN AF: 0.223

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.208

Gnomad OTH AF: 0.141

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

GnomAD4 genome AF: 0.165 AC: 25051 AN: 152058 Hom.: 2396 Cov.: 32 AF XY: 0.163 AC XY: 12123 AN XY: 74318

African (AFR) AF: 0.0801 AC: 3323 AN: 41504

American (AMR) AF: 0.189 AC: 2879 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.0979 AC: 339 AN: 3464

East Asian (EAS) AF: 0.192 AC: 988 AN: 5156

South Asian (SAS) AF: 0.133 AC: 642 AN: 4810

European-Finnish (FIN) AF: 0.223 AC: 2362 AN: 10570

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.208 AC: 14116 AN: 67976

Other (OTH) AF: 0.140 AC: 295 AN: 2112

Alfa AF: 0.183 Hom.: 7767

Bravo AF: 0.160

Asia WGS AF: 0.179 AC: 622 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.80
DANN	Benign	0.46
PhyloP100		-0.18

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs349114;

hg19: chr13-98203727;