rs13401620

Variant names:

• chr2-119755557-G-A
• rs13401620
• ENST00000747319.1:n.208+4075C>T

Your query was ambiguous. Multiple possible variants found:

• chr2-119755557-G-A
• chr2-119755557-G-C

Variant summary

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

The ENST00000747319.1(ENSG00000297359):​n.208+4075C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.258 in 150,614 control chromosomes in the GnomAD database, including 5,088 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 0.26 (5088 hom., cov: 28)
• Consequence: ENSG00000297359 ENST00000747319.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.198
• Publications: 11 publications found

Genes affected

ENSG00000297359 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.322 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101927764	XR_001739677.3	n.83+4075C>T		intron_variant	Intron 1 of 3
LOC101927764	XR_007087214.1	n.83+4075C>T		intron_variant	Intron 1 of 2
LOC101927764	XR_007087215.1	n.83+4075C>T		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000297359	ENST00000747319.1	n.208+4075C>T		intron_variant	Intron 1 of 2
ENSG00000297359	ENST00000747320.1	n.190+4075C>T		intron_variant	Intron 1 of 3
ENSG00000297359	ENST00000747321.1	n.168+4075C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.258 AC: 38800 AN: 150506 Hom.: 5075 Cov.: 28

Gnomad AFR AF: 0.248

Gnomad AMI AF: 0.212

Gnomad AMR AF: 0.256

Gnomad ASJ AF: 0.165

Gnomad EAS AF: 0.172

Gnomad SAS AF: 0.335

Gnomad FIN AF: 0.305

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.265

Gnomad OTH AF: 0.214

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

GnomAD4 genome AF: 0.258 AC: 38838 AN: 150614 Hom.: 5088 Cov.: 28 AF XY: 0.259 AC XY: 19045 AN XY: 73480

African (AFR) AF: 0.247 AC: 10131 AN: 40964

American (AMR) AF: 0.257 AC: 3902 AN: 15184

Ashkenazi Jewish (ASJ) AF: 0.165 AC: 572 AN: 3464

East Asian (EAS) AF: 0.171 AC: 880 AN: 5142

South Asian (SAS) AF: 0.336 AC: 1599 AN: 4756

European-Finnish (FIN) AF: 0.305 AC: 3093 AN: 10140

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.265 AC: 17956 AN: 67666

Other (OTH) AF: 0.217 AC: 456 AN: 2098

Alfa AF: 0.260 Hom.: 12927

Bravo AF: 0.254

Asia WGS AF: 0.276 AC: 963 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.3
DANN	Benign	0.45
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs13401620; hg19: chr2-120513133;