6-36660265-T-G

Variant names:

• chr6-36660265-T-G
• rs9462209
• ENST00000778909.1:n.192+416A>C

Variant summary

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

The ENST00000778909.1(ENSG00000301446):​n.192+416A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.554 in 152,110 control chromosomes in the GnomAD database, including 24,704 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 0.55 (24704 hom., cov: 32)
• Consequence: ENSG00000301446 ENST00000778909.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.84
• Publications: 18 publications found

Genes affected

ENSG00000301446 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.744 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
ENSG00000301446	ENST00000778909.1	n.192+416A>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.554 AC: 84173 AN: 151992 Hom.: 24654 Cov.: 32

Gnomad AFR AF: 0.751

Gnomad AMI AF: 0.447

Gnomad AMR AF: 0.589

Gnomad ASJ AF: 0.489

Gnomad EAS AF: 0.604

Gnomad SAS AF: 0.600

Gnomad FIN AF: 0.385

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.450

Gnomad OTH AF: 0.566

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

GnomAD4 genome AF: 0.554 AC: 84286 AN: 152110 Hom.: 24704 Cov.: 32 AF XY: 0.551 AC XY: 40994 AN XY: 74354

African (AFR) AF: 0.751 AC: 31172 AN: 41506

American (AMR) AF: 0.589 AC: 9003 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.489 AC: 1697 AN: 3472

East Asian (EAS) AF: 0.604 AC: 3115 AN: 5158

South Asian (SAS) AF: 0.600 AC: 2894 AN: 4826

European-Finnish (FIN) AF: 0.385 AC: 4069 AN: 10582

Middle Eastern (MID) AF: 0.551 AC: 162 AN: 294

European-Non Finnish (NFE) AF: 0.450 AC: 30558 AN: 67950

Other (OTH) AF: 0.571 AC: 1208 AN: 2116

Alfa AF: 0.494 Hom.: 44402

Bravo AF: 0.577

Asia WGS AF: 0.643 AC: 2237 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.34
DANN	Benign	0.28
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs9462209; hg19: chr6-36628042;