6-43800698-C-T

Variant names:

• chr6-43800698-C-T
• rs13211073
• ENST00000719551.1:n.192+3348C>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+3348C>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 5,075 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 (5075 hom., cov: 33)
• Consequence: ENSG00000283573 ENST00000719551.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.36
• Publications: 4 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=-1.05).
• 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

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000283573	ENST00000719551.1		n.192+3348C>T		intron	N/A
	ENSG00000283573	ENST00000719553.1		n.192+3348C>T		intron	N/A
	ENSG00000283573	ENST00000719555.1		n.159+3348C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.252 AC: 38344 AN: 152084 Hom.: 5071 Cov.: 33

Gnomad AFR AF: 0.182

Gnomad AMI AF: 0.173

Gnomad AMR AF: 0.300

Gnomad ASJ AF: 0.243

Gnomad EAS AF: 0.147

Gnomad SAS AF: 0.126

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: 38371 AN: 152202 Hom.: 5075 Cov.: 33 AF XY: 0.249 AC XY: 18556 AN XY: 74408

African (AFR) AF: 0.182 AC: 7570 AN: 41530

American (AMR) AF: 0.299 AC: 4573 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.243 AC: 843 AN: 3472

East Asian (EAS) AF: 0.148 AC: 766 AN: 5176

South Asian (SAS) AF: 0.126 AC: 608 AN: 4826

European-Finnish (FIN) AF: 0.276 AC: 2927 AN: 10586

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

European-Non Finnish (NFE) AF: 0.299 AC: 20349 AN: 68000

Other (OTH) AF: 0.251 AC: 532 AN: 2116

Alfa AF: 0.284 Hom.: 21692

Bravo AF: 0.252

Asia WGS AF: 0.148 AC: 513 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.036
DANN	Benign	0.16
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs13211073; hg19: chr6-43768435;