rs1205863

Variant names:

• chr6-11943293-T-G
• rs1205863
• ENST00000848130.1:n.334-8242T>G

Variant summary

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

The ENST00000848130.1(ENSG00000310201):​n.334-8242T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.304 in 152,156 control chromosomes in the GnomAD database, including 12,321 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 0.30 (12321 hom., cov: 32)
• Consequence: ENSG00000310201 ENST00000848130.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0510
• Publications: 8 publications found

Genes affected

ENSG00000310201 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.719 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000848130.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000310201	ENST00000848130.1		n.334-8242T>G		intron	N/A
	ENSG00000310201	ENST00000848131.1		n.238-8242T>G		intron	N/A
	ENSG00000310201	ENST00000848132.1		n.363-8242T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.303 AC: 46088 AN: 152038 Hom.: 12267 Cov.: 32

Gnomad AFR AF: 0.725

Gnomad AMI AF: 0.0197

Gnomad AMR AF: 0.192

Gnomad ASJ AF: 0.152

Gnomad EAS AF: 0.0556

Gnomad SAS AF: 0.0918

Gnomad FIN AF: 0.142

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.141

Gnomad OTH AF: 0.305

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

GnomAD4 genome AF: 0.304 AC: 46195 AN: 152156 Hom.: 12321 Cov.: 32 AF XY: 0.296 AC XY: 22006 AN XY: 74388

African (AFR) AF: 0.726 AC: 30109 AN: 41466

American (AMR) AF: 0.192 AC: 2937 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.152 AC: 527 AN: 3472

East Asian (EAS) AF: 0.0551 AC: 286 AN: 5188

South Asian (SAS) AF: 0.0915 AC: 442 AN: 4832

European-Finnish (FIN) AF: 0.142 AC: 1508 AN: 10586

Middle Eastern (MID) AF: 0.378 AC: 111 AN: 294

European-Non Finnish (NFE) AF: 0.141 AC: 9618 AN: 68010

Other (OTH) AF: 0.303 AC: 639 AN: 2112

Alfa AF: 0.381 Hom.: 7098

Bravo AF: 0.325

Asia WGS AF: 0.108 AC: 379 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.8
DANN	Benign	0.73
PhyloP100		-0.051

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1205863;

hg19: chr6-11943526;