6-32436358-A-G

Variant names:

• chr6-32436358-A-G
• rs5000563
• ENST00000766007.1:n.279+1786T>C

Variant summary

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

The ENST00000766007.1(ENSG00000299747):​n.279+1786T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.238 in 152,082 control chromosomes in the GnomAD database, including 4,884 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 0.24 (4884 hom., cov: 31)
• Consequence: ENSG00000299747 ENST00000766007.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.261
• Publications: 20 publications found

Genes affected

ENSG00000299747 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.285 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
ENSG00000299747	ENST00000766007.1	n.279+1786T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.238 AC: 36214 AN: 151964 Hom.: 4882 Cov.: 31

Gnomad AFR AF: 0.145

Gnomad AMI AF: 0.325

Gnomad AMR AF: 0.211

Gnomad ASJ AF: 0.149

Gnomad EAS AF: 0.161

Gnomad SAS AF: 0.175

Gnomad FIN AF: 0.413

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.289

Gnomad OTH AF: 0.237

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

GnomAD4 genome AF: 0.238 AC: 36237 AN: 152082 Hom.: 4884 Cov.: 31 AF XY: 0.241 AC XY: 17893 AN XY: 74298

African (AFR) AF: 0.145 AC: 6013 AN: 41508

American (AMR) AF: 0.211 AC: 3217 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.149 AC: 519 AN: 3472

East Asian (EAS) AF: 0.161 AC: 831 AN: 5172

South Asian (SAS) AF: 0.176 AC: 848 AN: 4822

European-Finnish (FIN) AF: 0.413 AC: 4359 AN: 10544

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.289 AC: 19628 AN: 67980

Other (OTH) AF: 0.234 AC: 495 AN: 2112

Alfa AF: 0.234 Hom.: 3158

Bravo AF: 0.220

Asia WGS AF: 0.203 AC: 710 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	8.8
DANN	Benign	0.86
PhyloP100		0.26

Splicing

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

Other links and lift over

dbSNP: rs5000563; hg19: chr6-32404135; COSMIC: COSV66623100;