6-94685568-T-C

Variant names:

• chr6-94685568-T-C
• rs4370337
• ENST00000689670.1:n.529+4517A>G

Variant summary

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

The ENST00000689670.1(ENSG00000289178):​n.529+4517A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.75 in 151,720 control chromosomes in the GnomAD database, including 42,905 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 0.75 (42905 hom., cov: 31)
• Consequence: ENSG00000289178 ENST00000689670.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0280

Genes affected

ENSG00000289178 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.873 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
ENSG00000289178	ENST00000689670.1	n.529+4517A>G		intron_variant	Intron 3 of 9
ENSG00000289178	ENST00000701797.1	n.295+4517A>G		intron_variant	Intron 2 of 9

Frequencies

GnomAD3 genomes AF: 0.750 AC: 113721 AN: 151604 Hom.: 42890 Cov.: 31

Gnomad AFR AF: 0.709

Gnomad AMI AF: 0.667

Gnomad AMR AF: 0.786

Gnomad ASJ AF: 0.672

Gnomad EAS AF: 0.894

Gnomad SAS AF: 0.762

Gnomad FIN AF: 0.838

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.748

Gnomad OTH AF: 0.734

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

GnomAD4 genome AF: 0.750 AC: 113784 AN: 151720 Hom.: 42905 Cov.: 31 AF XY: 0.753 AC XY: 55829 AN XY: 74120

Gnomad4 AFR AF: 0.708

Gnomad4 AMR AF: 0.787

Gnomad4 ASJ AF: 0.672

Gnomad4 EAS AF: 0.894

Gnomad4 SAS AF: 0.763

Gnomad4 FIN AF: 0.838

Gnomad4 NFE AF: 0.748

Gnomad4 OTH AF: 0.734

Alfa AF: 0.748 Hom.: 10968

Bravo AF: 0.747

Asia WGS AF: 0.816 AC: 2836 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.5
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4370337; hg19: chr6-95395286; COSMIC: COSV69414387;