6-94685568-T-C

Variant summary

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

The ENST00000701797.1(ENSG00000289178):n.295+4517A>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 0.75 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: ENST00000701797.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0280

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000701797.1	n.295+4517A>G		intron_variant, non_coding_transcript_variant
	ENST00000689670.1	n.529+4517A>G		intron_variant, non_coding_transcript_variant

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;