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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000719551.1. 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
	ENSG00000283573	ENST00000719551.1		n.192+3335A>T		intron	N/A
	ENSG00000283573	ENST00000719553.1		n.192+3335A>T		intron	N/A
	ENSG00000283573	ENST00000719555.1		n.159+3335A>T		intron	N/A

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 v4.9

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

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

Other links and lift over

dbSNP: rs13210960;

hg19: chr6-43768422;