rs13210960

Variant names:

• chr6-43800685-A-T
• rs13210960
• ENST00000719551.1:n.192+3335A>T

Variant summary

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

The ENST00000719551.1(ENSG00000283573):​n.192+3335A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.252 in 152,202 control chromosomes in the GnomAD database, including 5,074 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 0.25 (5074 hom., cov: 33)
• Consequence: ENSG00000283573 ENST00000719551.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17
• Publications: 3 publications found

Genes affected

ENSG00000283573 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.296 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375070	XR_007059588.1	n.192+3335A>T		intron_variant	Intron 1 of 2
LOC105375070	XR_007059589.1	n.192+3335A>T		intron_variant	Intron 1 of 2
LOC105375070	XR_926833.3	n.192+3335A>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000283573	ENST00000719551.1	n.192+3335A>T		intron_variant	Intron 1 of 2
ENSG00000283573	ENST00000719553.1	n.192+3335A>T		intron_variant	Intron 1 of 2
ENSG00000283573	ENST00000719555.1	n.159+3335A>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.252 AC: 38348 AN: 152084 Hom.: 5070 Cov.: 33

Gnomad AFR AF: 0.182

Gnomad AMI AF: 0.174

Gnomad AMR AF: 0.300

Gnomad ASJ AF: 0.243

Gnomad EAS AF: 0.148

Gnomad SAS AF: 0.130

Gnomad FIN AF: 0.276

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.299

Gnomad OTH AF: 0.253

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

GnomAD4 genome AF: 0.252 AC: 38376 AN: 152202 Hom.: 5074 Cov.: 33 AF XY: 0.249 AC XY: 18565 AN XY: 74412

African (AFR) AF: 0.182 AC: 7549 AN: 41514

American (AMR) AF: 0.299 AC: 4572 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.243 AC: 841 AN: 3468

East Asian (EAS) AF: 0.148 AC: 768 AN: 5180

South Asian (SAS) AF: 0.130 AC: 627 AN: 4822

European-Finnish (FIN) AF: 0.276 AC: 2929 AN: 10598

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.299 AC: 20353 AN: 67996

Other (OTH) AF: 0.252 AC: 532 AN: 2114

Alfa AF: 0.274 Hom.: 763

Bravo AF: 0.252

Asia WGS AF: 0.150 AC: 520 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.0060
DANN	Benign	0.61
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs13210960; hg19: chr6-43768422;