rs6922617

Variant names:

• chr6-41368363-G-A
• rs6922617
• ENST00000769987.1:n.518-582C>T

Variant summary

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

The ENST00000769987.1(ENSG00000300198):​n.518-582C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0611 in 152,226 control chromosomes in the GnomAD database, including 402 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 0.061 (402 hom., cov: 32)
• Consequence: ENSG00000300198 ENST00000769987.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.614
• Publications: 22 publications found

Genes affected

ENSG00000300198 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.232 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000769987.1. 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
	ENSG00000300198	ENST00000769987.1		n.518-582C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0611 AC: 9290 AN: 152108 Hom.: 398 Cov.: 32

Gnomad AFR AF: 0.0295

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0719

Gnomad ASJ AF: 0.0784

Gnomad EAS AF: 0.243

Gnomad SAS AF: 0.0938

Gnomad FIN AF: 0.0467

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0637

Gnomad OTH AF: 0.0675

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

GnomAD4 genome AF: 0.0611 AC: 9298 AN: 152226 Hom.: 402 Cov.: 32 AF XY: 0.0621 AC XY: 4620 AN XY: 74406

African (AFR) AF: 0.0295 AC: 1227 AN: 41552

American (AMR) AF: 0.0716 AC: 1096 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0784 AC: 272 AN: 3468

East Asian (EAS) AF: 0.243 AC: 1253 AN: 5162

South Asian (SAS) AF: 0.0934 AC: 450 AN: 4816

European-Finnish (FIN) AF: 0.0467 AC: 495 AN: 10596

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0637 AC: 4333 AN: 68018

Other (OTH) AF: 0.0735 AC: 155 AN: 2110

Alfa AF: 0.0638 Hom.: 1321

Bravo AF: 0.0625

Asia WGS AF: 0.181 AC: 632 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.1
DANN	Benign	0.63
PhyloP100		-0.61

Splicing

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

Other links and lift over

dbSNP: rs6922617; hg19: chr6-41336101;