rs6934928

Variant names:

• chr6-57987845-T-A
• rs6934928
• ENST00000641775.1:n.171+25597T>A

Variant summary

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

The ENST00000641775.1(ENSG00000225096):​n.171+25597T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.285 in 151,852 control chromosomes in the GnomAD database, including 6,684 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 0.29 (6684 hom., cov: 32)
• Consequence: ENSG00000225096 ENST00000641775.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.952
• Publications: 7 publications found

Genes affected

ENSG00000225096 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.358 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000641775.1. 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
	ENSG00000225096	ENST00000641775.1		n.171+25597T>A		intron	N/A
	ENSG00000225096	ENST00000641829.1		n.443+16189T>A		intron	N/A
	ENSG00000225096	ENST00000666847.1		n.124+25597T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.285 AC: 43283 AN: 151734 Hom.: 6677 Cov.: 32

Gnomad AFR AF: 0.363

Gnomad AMI AF: 0.191

Gnomad AMR AF: 0.218

Gnomad ASJ AF: 0.321

Gnomad EAS AF: 0.106

Gnomad SAS AF: 0.172

Gnomad FIN AF: 0.250

Gnomad MID AF: 0.252

Gnomad NFE AF: 0.280

Gnomad OTH AF: 0.286

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

GnomAD4 genome AF: 0.285 AC: 43318 AN: 151852 Hom.: 6684 Cov.: 32 AF XY: 0.278 AC XY: 20660 AN XY: 74270

African (AFR) AF: 0.363 AC: 14979 AN: 41268

American (AMR) AF: 0.218 AC: 3325 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.321 AC: 1110 AN: 3462

East Asian (EAS) AF: 0.106 AC: 548 AN: 5184

South Asian (SAS) AF: 0.172 AC: 827 AN: 4820

European-Finnish (FIN) AF: 0.250 AC: 2644 AN: 10566

Middle Eastern (MID) AF: 0.264 AC: 77 AN: 292

European-Non Finnish (NFE) AF: 0.280 AC: 19035 AN: 67976

Other (OTH) AF: 0.285 AC: 599 AN: 2102

Alfa AF: 0.281 Hom.: 831

Bravo AF: 0.290

Asia WGS AF: 0.167 AC: 579 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.33
DANN	Benign	0.38
PhyloP100		-0.95

Splicing

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

Other links and lift over

dbSNP: rs6934928; hg19: chr6-58314123;