rs2063201

Positions:

• chr6-105791510-C-T

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, non coding transcript 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: ENST00000644129.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.271

Genes affected

(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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000644129.1	n.281+38547G>A		intron_variant, non_coding_transcript_variant

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;