rs6034909

Variant names:

• chr20-1852009-A-G
• rs6034909
• ENST00000716594.1:n.950+38775T>C

Your query was ambiguous. Multiple possible variants found:

• chr20-1852009-A-G
• chr20-1852009-A-T

Variant summary

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

The ENST00000716594.1(ENSG00000286288):​n.950+38775T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.239 in 152,146 control chromosomes in the GnomAD database, including 4,927 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 0.24 (4927 hom., cov: 33)
• Consequence: ENSG00000286288 ENST00000716594.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.85
• Publications: 3 publications found

Genes affected

ENSG00000286288 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.395 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
ENSG00000286288	ENST00000716594.1	n.950+38775T>C		intron_variant	Intron 2 of 5
ENSG00000286288	ENST00000844949.1	n.102+23006T>C		intron_variant	Intron 1 of 2
ENSG00000286288	ENST00000844950.1	n.120+9758T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.239 AC: 36335 AN: 152026 Hom.: 4920 Cov.: 33

Gnomad AFR AF: 0.355

Gnomad AMI AF: 0.162

Gnomad AMR AF: 0.200

Gnomad ASJ AF: 0.360

Gnomad EAS AF: 0.409

Gnomad SAS AF: 0.200

Gnomad FIN AF: 0.165

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.172

Gnomad OTH AF: 0.263

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

GnomAD4 genome AF: 0.239 AC: 36377 AN: 152146 Hom.: 4927 Cov.: 33 AF XY: 0.237 AC XY: 17656 AN XY: 74386

African (AFR) AF: 0.355 AC: 14733 AN: 41502

American (AMR) AF: 0.199 AC: 3044 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.360 AC: 1247 AN: 3468

East Asian (EAS) AF: 0.409 AC: 2114 AN: 5164

South Asian (SAS) AF: 0.201 AC: 969 AN: 4824

European-Finnish (FIN) AF: 0.165 AC: 1742 AN: 10588

Middle Eastern (MID) AF: 0.432 AC: 127 AN: 294

European-Non Finnish (NFE) AF: 0.172 AC: 11699 AN: 67996

Other (OTH) AF: 0.262 AC: 554 AN: 2112

Alfa AF: 0.197 Hom.: 14060

Bravo AF: 0.250

Asia WGS AF: 0.283 AC: 982 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	5.3
DANN	Benign	0.65
PhyloP100		1.8

Splicing

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

Other links and lift over

dbSNP: rs6034909; hg19: chr20-1832655;