rs6065924

Variant names:

• chr20-46102124-G-A
• rs6065924
• ENST00000758803.1:n.235-103C>T

Your query was ambiguous. Multiple possible variants found:

• chr20-46102124-G-A
• chr20-46102124-G-T

Variant summary

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

The ENST00000758803.1(ENSG00000298900):​n.235-103C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.202 in 151,790 control chromosomes in the GnomAD database, including 3,415 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 0.20 (3415 hom., cov: 30)
• Consequence: ENSG00000298900 ENST00000758803.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.568
• Publications: 2 publications found

Genes affected

ENSG00000298900 (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 (SAS) allele frequency at 95% confidence interval = 0.297 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000758803.1. 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
	ENSG00000298900	ENST00000758803.1		n.235-103C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.202 AC: 30578 AN: 151672 Hom.: 3406 Cov.: 30

Gnomad AFR AF: 0.107

Gnomad AMI AF: 0.351

Gnomad AMR AF: 0.166

Gnomad ASJ AF: 0.276

Gnomad EAS AF: 0.286

Gnomad SAS AF: 0.309

Gnomad FIN AF: 0.245

Gnomad MID AF: 0.245

Gnomad NFE AF: 0.241

Gnomad OTH AF: 0.194

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

GnomAD4 genome AF: 0.202 AC: 30596 AN: 151790 Hom.: 3415 Cov.: 30 AF XY: 0.204 AC XY: 15089 AN XY: 74134

African (AFR) AF: 0.107 AC: 4433 AN: 41414

American (AMR) AF: 0.166 AC: 2526 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.276 AC: 956 AN: 3464

East Asian (EAS) AF: 0.286 AC: 1477 AN: 5166

South Asian (SAS) AF: 0.310 AC: 1483 AN: 4780

European-Finnish (FIN) AF: 0.245 AC: 2571 AN: 10500

Middle Eastern (MID) AF: 0.240 AC: 70 AN: 292

European-Non Finnish (NFE) AF: 0.241 AC: 16347 AN: 67916

Other (OTH) AF: 0.197 AC: 414 AN: 2106

Alfa AF: 0.148 Hom.: 380

Bravo AF: 0.192

Asia WGS AF: 0.243 AC: 846 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	10
DANN	Benign	0.71
PhyloP100		0.57

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: rs6065924;

hg19: chr20-44730763;