3-176312308-G-T

Variant names:

• chr3-176312308-G-T
• rs6799767
• ENST00000687649.2:n.430+6120C>A

Variant summary

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

The ENST00000687649.2(ENSG00000288895):​n.430+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 ENST00000687649.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.695
• Publications: 11 publications found

Genes affected

ENSG00000288895 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000687649.2. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000288895	ENST00000687649.2		n.430+6120C>A		intron	N/A
	ENSG00000288895	ENST00000803480.1		n.274+12505C>A		intron	N/A
	ENSG00000288895	ENST00000803481.1		n.435+6120C>A		intron	N/A

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

African (AFR) AF: 0.422 AC: 17476 AN: 41402

American (AMR) AF: 0.483 AC: 7382 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.553 AC: 1917 AN: 3466

East Asian (EAS) AF: 0.367 AC: 1896 AN: 5160

South Asian (SAS) AF: 0.454 AC: 2186 AN: 4816

European-Finnish (FIN) AF: 0.721 AC: 7616 AN: 10560

Middle Eastern (MID) AF: 0.429 AC: 126 AN: 294

European-Non Finnish (NFE) AF: 0.601 AC: 40816 AN: 67940

Other (OTH) AF: 0.533 AC: 1123 AN: 2108

Alfa AF: 0.566 Hom.: 113885

Bravo AF: 0.511

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.13
DANN	Benign	0.40
PhyloP100		-0.69

Splicing

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

Other links and lift over

dbSNP: rs6799767; hg19: chr3-176030096;