rs6929568

Positions:

• chr6-8228709-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000642149.1(ENSG00000232234):​n.207-10222T>G variant causes a intron, non coding transcript 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: ENST00000642149.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.318

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC105374910	XR_001743950.2	n.188-10222T>G		intron_variant, non_coding_transcript_variant
LOC105374910	XR_926440.3	n.81-1405T>G		intron_variant, non_coding_transcript_variant
LOC105374910	XR_926441.3	n.188-10222T>G		intron_variant, non_coding_transcript_variant
LOC105374910	XR_926443.3	n.81-10222T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000642149.1	n.207-10222T>G		intron_variant, non_coding_transcript_variant
	ENST00000439891.3	n.61-1405T>G		intron_variant, non_coding_transcript_variant		5
	ENST00000643749.1	n.143-10222T>G		intron_variant, non_coding_transcript_variant
	ENST00000647315.1	n.180-10222T>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.514

Gnomad4 AMR AF: 0.303

Gnomad4 ASJ AF: 0.388

Gnomad4 EAS AF: 0.384

Gnomad4 SAS AF: 0.287

Gnomad4 FIN AF: 0.243

Gnomad4 NFE AF: 0.318

Gnomad4 OTH AF: 0.388

Alfa AF: 0.333 Hom.: 1864

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6929568; hg19: chr6-8228942;