rs6929568

Variant names:

• chr6-8228709-T-G
• rs6929568
• ENST00000439891.3:n.61-1405T>G

Variant summary

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

The ENST00000439891.3(ENSG00000232234):​n.61-1405T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.369 in 152,020 control chromosomes in the GnomAD database, including 11,060 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 0.37 (11060 hom., cov: 32)
• Consequence: ENSG00000232234 ENST00000439891.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.318
• Publications: 8 publications found

Genes affected

ENSG00000232234 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.509 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105374910	XR_001743950.2	n.188-10222T>G		intron_variant	Intron 2 of 3
LOC105374910	XR_926440.3	n.81-1405T>G		intron_variant	Intron 1 of 3
LOC105374910	XR_926441.3	n.188-10222T>G		intron_variant	Intron 2 of 3
LOC105374910	XR_926443.3	n.81-10222T>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000232234	ENST00000439891.3	n.61-1405T>G		intron_variant	Intron 1 of 6	5
ENSG00000232234	ENST00000642149.1	n.207-10222T>G		intron_variant	Intron 2 of 5
ENSG00000232234	ENST00000643749.1	n.143-10222T>G		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.369 AC: 55994 AN: 151902 Hom.: 11042 Cov.: 32

Gnomad AFR AF: 0.514

Gnomad AMI AF: 0.328

Gnomad AMR AF: 0.303

Gnomad ASJ AF: 0.388

Gnomad EAS AF: 0.384

Gnomad SAS AF: 0.288

Gnomad FIN AF: 0.243

Gnomad MID AF: 0.363

Gnomad NFE AF: 0.318

Gnomad OTH AF: 0.390

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

GnomAD4 genome AF: 0.369 AC: 56049 AN: 152020 Hom.: 11060 Cov.: 32 AF XY: 0.362 AC XY: 26902 AN XY: 74292

African (AFR) AF: 0.514 AC: 21309 AN: 41422

American (AMR) AF: 0.303 AC: 4631 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.388 AC: 1347 AN: 3470

East Asian (EAS) AF: 0.384 AC: 1984 AN: 5162

South Asian (SAS) AF: 0.287 AC: 1382 AN: 4812

European-Finnish (FIN) AF: 0.243 AC: 2568 AN: 10568

Middle Eastern (MID) AF: 0.349 AC: 102 AN: 292

European-Non Finnish (NFE) AF: 0.318 AC: 21607 AN: 67980

Other (OTH) AF: 0.388 AC: 820 AN: 2116

Alfa AF: 0.337 Hom.: 1974

Bravo AF: 0.378

Asia WGS AF: 0.329 AC: 1144 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	6.8
DANN	Benign	0.48
PhyloP100		0.32

Splicing

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

Other links and lift over

dbSNP: rs6929568; hg19: chr6-8228942;