chr6-100890932-T-A

Variant names:

• chr6-100890932-T-A
• rs9390700
• ENST00000801155.1:n.308+553T>A

Variant summary

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

The ENST00000801155.1(ENSG00000260000):​n.308+553T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0238 in 152,288 control chromosomes in the GnomAD database, including 295 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 0.024 (295 hom., cov: 33)
• Consequence: ENSG00000260000 ENST00000801155.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.588
• Publications: 0 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=-0.47).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.279 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107984041	XR_002956381.2	n.199-1066T>A		intron_variant	Intron 1 of 6
LOC107984041	XR_002956382.2	n.199-1066T>A		intron_variant	Intron 1 of 3
LOC107984041	XR_007059692.1	n.199-1066T>A		intron_variant	Intron 1 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000260000	ENST00000801155.1	n.308+553T>A		intron_variant	Intron 1 of 2
ENSG00000260000	ENST00000801152.1	n.*91T>A		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.0238 AC: 3626 AN: 152170 Hom.: 296 Cov.: 33

Gnomad AFR AF: 0.00623

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0553

Gnomad ASJ AF: 0.0208

Gnomad EAS AF: 0.292

Gnomad SAS AF: 0.0445

Gnomad FIN AF: 0.0221

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.00629

Gnomad OTH AF: 0.0258

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

GnomAD4 genome AF: 0.0238 AC: 3629 AN: 152288 Hom.: 295 Cov.: 33 AF XY: 0.0267 AC XY: 1991 AN XY: 74470

African (AFR) AF: 0.00621 AC: 258 AN: 41560

American (AMR) AF: 0.0559 AC: 855 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0208 AC: 72 AN: 3468

East Asian (EAS) AF: 0.291 AC: 1505 AN: 5174

South Asian (SAS) AF: 0.0448 AC: 216 AN: 4824

European-Finnish (FIN) AF: 0.0221 AC: 235 AN: 10622

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.00626 AC: 426 AN: 68022

Other (OTH) AF: 0.0260 AC: 55 AN: 2116

Alfa AF: 0.0134 Hom.: 10

Bravo AF: 0.0297

Asia WGS AF: 0.148 AC: 512 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.47
CADD	Benign	11
DANN	Benign	0.96
PhyloP100		-0.59

Splicing

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

Other links and lift over

dbSNP: rs9390700; hg19: chr6-101338808;