rs6060965

Variant names:

• chr20-31818295-A-G
• rs6060965
• ENST00000769779.1:n.*237A>G

Variant summary

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

The ENST00000769779.1(ENSG00000300178):​n.*237A>G variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0877 in 152,162 control chromosomes in the GnomAD database, including 660 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 0.088 (660 hom., cov: 32)
• Consequence: ENSG00000300178 ENST00000769779.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.715
• Publications: 5 publications found

Genes affected

ENSG00000300178 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.134 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
ENSG00000300178	ENST00000769779.1	n.*237A>G		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.0875 AC: 13306 AN: 152044 Hom.: 657 Cov.: 32

Gnomad AFR AF: 0.136

Gnomad AMI AF: 0.0822

Gnomad AMR AF: 0.0621

Gnomad ASJ AF: 0.0855

Gnomad EAS AF: 0.000963

Gnomad SAS AF: 0.0268

Gnomad FIN AF: 0.0729

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0766

Gnomad OTH AF: 0.0963

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

GnomAD4 genome AF: 0.0877 AC: 13340 AN: 152162 Hom.: 660 Cov.: 32 AF XY: 0.0849 AC XY: 6317 AN XY: 74400

African (AFR) AF: 0.137 AC: 5671 AN: 41490

American (AMR) AF: 0.0619 AC: 946 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0855 AC: 297 AN: 3472

East Asian (EAS) AF: 0.000966 AC: 5 AN: 5178

South Asian (SAS) AF: 0.0272 AC: 131 AN: 4816

European-Finnish (FIN) AF: 0.0729 AC: 773 AN: 10600

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.0766 AC: 5208 AN: 68016

Other (OTH) AF: 0.0957 AC: 202 AN: 2110

Alfa AF: 0.0822 Hom.: 115

Bravo AF: 0.0902

Asia WGS AF: 0.0200 AC: 69 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.71
DANN	Benign	0.42
PhyloP100		-0.71

Splicing

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

Other links and lift over

dbSNP: rs6060965; hg19: chr20-30406098;