rs349114

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370324	XR_007063845.1	n.2615-4122C>T		intron_variant	Intron 3 of 5
LOC105370324	XR_931663.3	n.2671-4122C>T		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000304344	ENST00000802609.1	n.68-4122C>T		intron_variant	Intron 1 of 2
ENSG00000304344	ENST00000802610.1	n.135-4122C>T		intron_variant	Intron 2 of 3
ENSG00000304344	ENST00000802611.1	n.139-4122C>T		intron_variant	Intron 2 of 4

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 v4.3

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

Other links and lift over

dbSNP: rs349114; hg19: chr13-98203727;