rs305067

Variant names:

• chr16-85938234-C-G
• rs305067
• ENST00000645383.1:n.393+5960C>G

Your query was ambiguous. Multiple possible variants found:

• chr16-85938234-C-G
• chr16-85938234-C-T

Variant summary

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

The ENST00000645383.1(ENSG00000285163):​n.393+5960C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.751 in 152,092 control chromosomes in the GnomAD database, including 44,080 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 (44080 hom., cov: 31)
• Consequence: ENSG00000285163 ENST00000645383.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.829

Genes affected

ENSG00000285163 (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 (AFR) allele frequency at 95% confidence interval = 0.906 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
ENSG00000285163	ENST00000645383.1	n.393+5960C>G		intron_variant	Intron 1 of 3
ENSG00000285163	ENST00000646214.1	n.78-7182C>G		intron_variant	Intron 1 of 3
ENSG00000285163	ENST00000646986.1	n.715+2223C>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.751 AC: 114121 AN: 151974 Hom.: 44013 Cov.: 31

Gnomad AFR AF: 0.914

Gnomad AMI AF: 0.686

Gnomad AMR AF: 0.748

Gnomad ASJ AF: 0.598

Gnomad EAS AF: 0.865

Gnomad SAS AF: 0.770

Gnomad FIN AF: 0.784

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.648

Gnomad OTH AF: 0.693

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

GnomAD4 genome AF: 0.751 AC: 114255 AN: 152092 Hom.: 44080 Cov.: 31 AF XY: 0.757 AC XY: 56305 AN XY: 74332

Gnomad4 AFR AF: 0.914

Gnomad4 AMR AF: 0.748

Gnomad4 ASJ AF: 0.598

Gnomad4 EAS AF: 0.866

Gnomad4 SAS AF: 0.771

Gnomad4 FIN AF: 0.784

Gnomad4 NFE AF: 0.648

Gnomad4 OTH AF: 0.695

Alfa AF: 0.706 Hom.: 4568

Bravo AF: 0.754

Asia WGS AF: 0.833 AC: 2892 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.3
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs305067; hg19: chr16-85971840;