6-36665292-A-G

Variant names:

• chr6-36665292-A-G
• rs4713999
• ENST00000777596.1:n.354-1025T>C

Variant summary

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

The ENST00000777596.1(ENSG00000301272):​n.354-1025T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.644 in 151,930 control chromosomes in the GnomAD database, including 31,779 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 0.64 (31779 hom., cov: 31)
• Consequence: ENSG00000301272 ENST00000777596.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.424
• Publications: 17 publications found

Genes affected

ENSG00000301272 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.702 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
ENSG00000301272	ENST00000777596.1	n.354-1025T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.644 AC: 97835 AN: 151812 Hom.: 31754 Cov.: 31

Gnomad AFR AF: 0.621

Gnomad AMI AF: 0.799

Gnomad AMR AF: 0.678

Gnomad ASJ AF: 0.440

Gnomad EAS AF: 0.722

Gnomad SAS AF: 0.617

Gnomad FIN AF: 0.678

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.653

Gnomad OTH AF: 0.595

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

GnomAD4 genome AF: 0.644 AC: 97896 AN: 151930 Hom.: 31779 Cov.: 31 AF XY: 0.644 AC XY: 47860 AN XY: 74260

African (AFR) AF: 0.620 AC: 25668 AN: 41374

American (AMR) AF: 0.679 AC: 10369 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.440 AC: 1527 AN: 3470

East Asian (EAS) AF: 0.721 AC: 3732 AN: 5174

South Asian (SAS) AF: 0.617 AC: 2973 AN: 4818

European-Finnish (FIN) AF: 0.678 AC: 7139 AN: 10532

Middle Eastern (MID) AF: 0.510 AC: 150 AN: 294

European-Non Finnish (NFE) AF: 0.653 AC: 44364 AN: 67966

Other (OTH) AF: 0.589 AC: 1245 AN: 2112

Alfa AF: 0.634 Hom.: 23266

Bravo AF: 0.646

Asia WGS AF: 0.639 AC: 2220 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.48
PhyloP100		-0.42

Splicing

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

Other links and lift over

dbSNP: rs4713999; hg19: chr6-36633069;