3-176312308-G-T

Variant names:

• chr3-176312308-G-T
• rs6799767
• ENST00000687649.1:n.413+6120C>A

Variant summary

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

The ENST00000687649.1(ENSG00000288895):​n.413+6120C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.533 in 151,938 control chromosomes in the GnomAD database, including 22,247 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 0.53 (22247 hom., cov: 32)
• Consequence: ENSG00000288895 ENST00000687649.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.695

Genes affected

ENSG00000288895 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.596 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
ENSG00000288895	ENST00000687649.1	n.413+6120C>A		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.533 AC: 80976 AN: 151818 Hom.: 22244 Cov.: 32

Gnomad AFR AF: 0.422

Gnomad AMI AF: 0.523

Gnomad AMR AF: 0.483

Gnomad ASJ AF: 0.553

Gnomad EAS AF: 0.367

Gnomad SAS AF: 0.454

Gnomad FIN AF: 0.721

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.601

Gnomad OTH AF: 0.537

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

GnomAD4 genome AF: 0.533 AC: 81015 AN: 151938 Hom.: 22247 Cov.: 32 AF XY: 0.536 AC XY: 39790 AN XY: 74240

Gnomad4 AFR AF: 0.422

Gnomad4 AMR AF: 0.483

Gnomad4 ASJ AF: 0.553

Gnomad4 EAS AF: 0.367

Gnomad4 SAS AF: 0.454

Gnomad4 FIN AF: 0.721

Gnomad4 NFE AF: 0.601

Gnomad4 OTH AF: 0.533

Alfa AF: 0.572 Hom.: 56955

Bravo AF: 0.511

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.13
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6799767; hg19: chr3-176030096;