rs6076960

Variant names:

• chr20-6205510-A-C
• rs6076960
• ENST00000812818.1:n.235+6309T>G

Variant summary

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

The ENST00000812818.1(ENSG00000305761):​n.235+6309T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.472 in 151,918 control chromosomes in the GnomAD database, including 17,396 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 0.47 (17396 hom., cov: 32)
• Consequence: ENSG00000305761 ENST00000812818.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.164
• Publications: 1 publications found

Genes affected

ENSG00000305761 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.515 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000812818.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000305761	ENST00000812818.1		n.235+6309T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.472 AC: 71666 AN: 151800 Hom.: 17385 Cov.: 32

Gnomad AFR AF: 0.423

Gnomad AMI AF: 0.532

Gnomad AMR AF: 0.402

Gnomad ASJ AF: 0.568

Gnomad EAS AF: 0.223

Gnomad SAS AF: 0.455

Gnomad FIN AF: 0.540

Gnomad MID AF: 0.655

Gnomad NFE AF: 0.520

Gnomad OTH AF: 0.499

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

GnomAD4 genome AF: 0.472 AC: 71714 AN: 151918 Hom.: 17396 Cov.: 32 AF XY: 0.469 AC XY: 34803 AN XY: 74214

African (AFR) AF: 0.424 AC: 17550 AN: 41438

American (AMR) AF: 0.401 AC: 6131 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.568 AC: 1970 AN: 3470

East Asian (EAS) AF: 0.223 AC: 1157 AN: 5182

South Asian (SAS) AF: 0.457 AC: 2201 AN: 4816

European-Finnish (FIN) AF: 0.540 AC: 5678 AN: 10524

Middle Eastern (MID) AF: 0.653 AC: 192 AN: 294

European-Non Finnish (NFE) AF: 0.520 AC: 35308 AN: 67898

Other (OTH) AF: 0.493 AC: 1043 AN: 2114

Alfa AF: 0.504 Hom.: 13021

Bravo AF: 0.456

Asia WGS AF: 0.334 AC: 1157 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	12
DANN	Benign	0.94
PhyloP100		0.16

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6076960;

hg19: chr20-6186157;