chr6-100888006-G-C

Variant names:

• chr6-100888006-G-C
• rs846798
• ENST00000801152.1:n.171-1378G>C

Variant summary

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

The ENST00000801152.1(ENSG00000260000):​n.171-1378G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.712 in 151,880 control chromosomes in the GnomAD database, including 38,739 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 0.71 (38739 hom., cov: 30)
• Consequence: ENSG00000260000 ENST00000801152.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29
• Publications: 2 publications found

Genes affected

ENSG00000260000 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.731 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000801152.1. 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
	ENSG00000260000	ENST00000801152.1		n.171-1378G>C		intron	N/A
	ENSG00000260000	ENST00000801153.1		n.176-1378G>C		intron	N/A
	ENSG00000260000	ENST00000801154.1		n.174-1375G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.712 AC: 108054 AN: 151762 Hom.: 38693 Cov.: 30

Gnomad AFR AF: 0.713

Gnomad AMI AF: 0.798

Gnomad AMR AF: 0.720

Gnomad ASJ AF: 0.779

Gnomad EAS AF: 0.751

Gnomad SAS AF: 0.482

Gnomad FIN AF: 0.726

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.716

Gnomad OTH AF: 0.706

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

GnomAD4 genome AF: 0.712 AC: 108159 AN: 151880 Hom.: 38739 Cov.: 30 AF XY: 0.706 AC XY: 52390 AN XY: 74198

African (AFR) AF: 0.714 AC: 29554 AN: 41412

American (AMR) AF: 0.721 AC: 11005 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.779 AC: 2697 AN: 3464

East Asian (EAS) AF: 0.751 AC: 3880 AN: 5168

South Asian (SAS) AF: 0.482 AC: 2317 AN: 4808

European-Finnish (FIN) AF: 0.726 AC: 7614 AN: 10492

Middle Eastern (MID) AF: 0.711 AC: 209 AN: 294

European-Non Finnish (NFE) AF: 0.716 AC: 48656 AN: 67944

Other (OTH) AF: 0.709 AC: 1501 AN: 2116

Alfa AF: 0.714 Hom.: 4579

Bravo AF: 0.721

Asia WGS AF: 0.620 AC: 2154 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.30
DANN	Benign	0.39
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs846798; hg19: chr6-101335882; COSMIC: COSV74095592;