rs6085143

Variant names:

• chr20-5398840-G-C
• rs6085143
• ENST00000668553.1:n.1121-7398G>C

Your query was ambiguous. Multiple possible variants found:

• chr20-5398840-G-C
• chr20-5398840-G-T

Variant summary

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

The ENST00000668553.1(ENSG00000230563):​n.1121-7398G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.231 in 152,066 control chromosomes in the GnomAD database, including 4,269 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 0.23 (4269 hom., cov: 32)
• Consequence: ENSG00000230563 ENST00000668553.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0640
• Publications: 1 publications found

Genes affected

ENSG00000230563 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.261 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
ENSG00000230563	ENST00000668553.1	n.1121-7398G>C		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.232 AC: 35187 AN: 151948 Hom.: 4265 Cov.: 32

Gnomad AFR AF: 0.163

Gnomad AMI AF: 0.292

Gnomad AMR AF: 0.254

Gnomad ASJ AF: 0.252

Gnomad EAS AF: 0.194

Gnomad SAS AF: 0.266

Gnomad FIN AF: 0.245

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.264

Gnomad OTH AF: 0.239

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

GnomAD4 genome AF: 0.231 AC: 35199 AN: 152066 Hom.: 4269 Cov.: 32 AF XY: 0.232 AC XY: 17248 AN XY: 74344

African (AFR) AF: 0.163 AC: 6758 AN: 41486

American (AMR) AF: 0.255 AC: 3889 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.252 AC: 874 AN: 3462

East Asian (EAS) AF: 0.195 AC: 1003 AN: 5152

South Asian (SAS) AF: 0.266 AC: 1284 AN: 4824

European-Finnish (FIN) AF: 0.245 AC: 2596 AN: 10594

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.264 AC: 17959 AN: 67964

Other (OTH) AF: 0.238 AC: 502 AN: 2110

Alfa AF: 0.123 Hom.: 206

Bravo AF: 0.229

Asia WGS AF: 0.242 AC: 841 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.0
DANN	Benign	0.70
PhyloP100		-0.064

Splicing

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

Other links and lift over

dbSNP: rs6085143; hg19: chr20-5379486;