rs2063201

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000284999 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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

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

Gnomad4 AFR AF: 0.547

Gnomad4 AMR AF: 0.717

Gnomad4 ASJ AF: 0.678

Gnomad4 EAS AF: 0.601

Gnomad4 SAS AF: 0.675

Gnomad4 FIN AF: 0.609

Gnomad4 NFE AF: 0.670

Gnomad4 OTH AF: 0.642

Alfa AF: 0.663 Hom.: 55523

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2063201; hg19: chr6-106239385;