6-100488889-C-T

Variant names:

• chr6-100488889-C-T
• rs7766596
• ENST00000835850.1:n.137+3975C>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000835850.1(ENSG00000308693):​n.137+3975C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.854 in 152,216 control chromosomes in the GnomAD database, including 55,879 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 0.85 (55879 hom., cov: 33)
• Consequence: ENSG00000308693 ENST00000835850.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0800
• Publications: 1 publications found

Genes affected

ENSG00000308693 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.4).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.939 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000308693	ENST00000835850.1	n.137+3975C>T		intron_variant	Intron 1 of 2
ENSG00000308693	ENST00000835851.1	n.148-3242C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.854 AC: 129941 AN: 152098 Hom.: 55834 Cov.: 33

Gnomad AFR AF: 0.946

Gnomad AMI AF: 0.730

Gnomad AMR AF: 0.856

Gnomad ASJ AF: 0.709

Gnomad EAS AF: 0.868

Gnomad SAS AF: 0.928

Gnomad FIN AF: 0.810

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.809

Gnomad OTH AF: 0.822

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

GnomAD4 genome AF: 0.854 AC: 130037 AN: 152216 Hom.: 55879 Cov.: 33 AF XY: 0.857 AC XY: 63779 AN XY: 74406

African (AFR) AF: 0.946 AC: 39312 AN: 41538

American (AMR) AF: 0.856 AC: 13078 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.709 AC: 2461 AN: 3472

East Asian (EAS) AF: 0.867 AC: 4496 AN: 5186

South Asian (SAS) AF: 0.928 AC: 4475 AN: 4820

European-Finnish (FIN) AF: 0.810 AC: 8563 AN: 10578

Middle Eastern (MID) AF: 0.748 AC: 220 AN: 294

European-Non Finnish (NFE) AF: 0.809 AC: 55047 AN: 68020

Other (OTH) AF: 0.814 AC: 1721 AN: 2114

Alfa AF: 0.819 Hom.: 63483

Bravo AF: 0.859

Asia WGS AF: 0.881 AC: 3066 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.40
CADD	Benign	1.2
DANN	Benign	0.64
PhyloP100		-0.080

Splicing

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

Other links and lift over

dbSNP: rs7766596; hg19: chr6-100936765;