rs6065925

Variant names:

• chr20-46105657-G-A
• rs6065925
• ENST00000758803.1:n.234+3101C>T

Variant summary

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

The ENST00000758803.1(ENSG00000298900):​n.234+3101C>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 152,150 control chromosomes in the GnomAD database, including 3,449 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 (3449 hom., cov: 32)
• Consequence: ENSG00000298900 ENST00000758803.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.713
• Publications: 16 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=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.298 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
ENSG00000298900	ENST00000758803.1	n.234+3101C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.202 AC: 30687 AN: 152032 Hom.: 3441 Cov.: 32

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: 0.310

Gnomad FIN AF: 0.245

Gnomad MID AF: 0.244

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: 30704 AN: 152150 Hom.: 3449 Cov.: 32 AF XY: 0.204 AC XY: 15153 AN XY: 74384

African (AFR) AF: 0.107 AC: 4458 AN: 41512

American (AMR) AF: 0.166 AC: 2538 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.276 AC: 959 AN: 3472

East Asian (EAS) AF: 0.286 AC: 1482 AN: 5178

South Asian (SAS) AF: 0.311 AC: 1503 AN: 4828

European-Finnish (FIN) AF: 0.245 AC: 2585 AN: 10564

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.241 AC: 16374 AN: 67988

Other (OTH) AF: 0.196 AC: 415 AN: 2114

Alfa AF: 0.230 Hom.: 18206

Bravo AF: 0.192

Asia WGS AF: 0.243 AC: 848 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.5
DANN	Benign	0.68
PhyloP100		0.71

Splicing

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

Other links and lift over

dbSNP: rs6065925; hg19: chr20-44734296;