rs6934928

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000225096 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000225096	ENST00000641775.1	n.171+25597T>A		intron_variant	Intron 1 of 5
ENSG00000225096	ENST00000641829.1	n.443+16189T>A		intron_variant	Intron 4 of 7
ENSG00000225096	ENST00000666847.1	n.124+25597T>A		intron_variant	Intron 1 of 4

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

Gnomad4 AFR AF: 0.363

Gnomad4 AMR AF: 0.218

Gnomad4 ASJ AF: 0.321

Gnomad4 EAS AF: 0.106

Gnomad4 SAS AF: 0.172

Gnomad4 FIN AF: 0.250

Gnomad4 NFE AF: 0.280

Gnomad4 OTH AF: 0.285

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6934928; hg19: chr6-58314123;