rs2063201

Variant names:

• chr6-105791510-C-T
• rs2063201
• ENST00000644129.1:n.281+38547G>A

Variant summary

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

The ENST00000644129.1(ENSG00000284999):​n.281+38547G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.634 in 152,066 control chromosomes in the GnomAD database, including 30,963 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 0.63 (30963 hom., cov: 33)
• Consequence: ENSG00000284999 ENST00000644129.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.271
• Publications: 2 publications found

Genes affected

ENSG00000284999 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.706 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
ENSG00000284999	ENST00000644129.1	n.281+38547G>A		intron_variant	Intron 3 of 3
ENSG00000284999	ENST00000744159.1	n.375-21915G>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.634 AC: 96354 AN: 151948 Hom.: 30927 Cov.: 33

Gnomad AFR AF: 0.546

Gnomad AMI AF: 0.645

Gnomad AMR AF: 0.717

Gnomad ASJ AF: 0.678

Gnomad EAS AF: 0.602

Gnomad SAS AF: 0.675

Gnomad FIN AF: 0.609

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.670

Gnomad OTH AF: 0.638

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

GnomAD4 genome AF: 0.634 AC: 96435 AN: 152066 Hom.: 30963 Cov.: 33 AF XY: 0.633 AC XY: 47077 AN XY: 74358

African (AFR) AF: 0.547 AC: 22644 AN: 41432

American (AMR) AF: 0.717 AC: 10964 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.678 AC: 2353 AN: 3470

East Asian (EAS) AF: 0.601 AC: 3115 AN: 5182

South Asian (SAS) AF: 0.675 AC: 3255 AN: 4820

European-Finnish (FIN) AF: 0.609 AC: 6432 AN: 10566

Middle Eastern (MID) AF: 0.636 AC: 187 AN: 294

European-Non Finnish (NFE) AF: 0.670 AC: 45542 AN: 67994

Other (OTH) AF: 0.642 AC: 1356 AN: 2112

Alfa AF: 0.658 Hom.: 130373

Bravo AF: 0.637

Asia WGS AF: 0.664 AC: 2312 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	6.1
DANN	Benign	0.76
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs2063201; hg19: chr6-106239385;