6-15873758-G-T

Variant names:

• chr6-15873758-G-T
• rs1000117
• ENST00000806821.1:n.448+19206G>T

Variant summary

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

The ENST00000806821.1(ENSG00000289953):​n.448+19206G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.667 in 152,066 control chromosomes in the GnomAD database, including 34,098 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 0.67 (34098 hom., cov: 32)
• Consequence: ENSG00000289953 ENST00000806821.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0380
• Publications: 1 publications found

Genes affected

ENSG00000289953 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.696 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000806821.1. 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
	ENSG00000289953	ENST00000806821.1		n.448+19206G>T		intron	N/A
	ENSG00000289953	ENST00000806822.1		n.462+19206G>T		intron	N/A
	ENSG00000289953	ENST00000806823.1		n.302+19206G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.667 AC: 101373 AN: 151948 Hom.: 34082 Cov.: 32

Gnomad AFR AF: 0.599

Gnomad AMI AF: 0.844

Gnomad AMR AF: 0.708

Gnomad ASJ AF: 0.782

Gnomad EAS AF: 0.585

Gnomad SAS AF: 0.604

Gnomad FIN AF: 0.692

Gnomad MID AF: 0.737

Gnomad NFE AF: 0.697

Gnomad OTH AF: 0.700

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

GnomAD4 genome AF: 0.667 AC: 101437 AN: 152066 Hom.: 34098 Cov.: 32 AF XY: 0.667 AC XY: 49611 AN XY: 74338

African (AFR) AF: 0.598 AC: 24798 AN: 41438

American (AMR) AF: 0.708 AC: 10824 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.782 AC: 2713 AN: 3470

East Asian (EAS) AF: 0.585 AC: 3026 AN: 5170

South Asian (SAS) AF: 0.604 AC: 2909 AN: 4818

European-Finnish (FIN) AF: 0.692 AC: 7308 AN: 10560

Middle Eastern (MID) AF: 0.738 AC: 217 AN: 294

European-Non Finnish (NFE) AF: 0.697 AC: 47393 AN: 67992

Other (OTH) AF: 0.699 AC: 1479 AN: 2116

Alfa AF: 0.683 Hom.: 7406

Bravo AF: 0.668

Asia WGS AF: 0.546 AC: 1895 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	8.3
DANN	Benign	0.68
PhyloP100		-0.038

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: rs1000117;

hg19: chr6-15873989;