rs3129868

Variant names:

• chr6-32436600-A-C
• rs3129868
• ENST00000766007.1:n.279+1544T>G

Variant summary

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

The ENST00000766007.1(ENSG00000299747):​n.279+1544T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.894 in 152,122 control chromosomes in the GnomAD database, including 60,917 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 0.89 (60917 hom., cov: 31)
• Consequence: ENSG00000299747 ENST00000766007.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.93
• Publications: 44 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.943 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+1544T>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.894 AC: 135865 AN: 152004 Hom.: 60863 Cov.: 31

Gnomad AFR AF: 0.951

Gnomad AMI AF: 0.913

Gnomad AMR AF: 0.919

Gnomad ASJ AF: 0.933

Gnomad EAS AF: 0.885

Gnomad SAS AF: 0.883

Gnomad FIN AF: 0.871

Gnomad MID AF: 0.924

Gnomad NFE AF: 0.855

Gnomad OTH AF: 0.916

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

GnomAD4 genome AF: 0.894 AC: 135978 AN: 152122 Hom.: 60917 Cov.: 31 AF XY: 0.893 AC XY: 66433 AN XY: 74364

African (AFR) AF: 0.951 AC: 39497 AN: 41518

American (AMR) AF: 0.919 AC: 14029 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.933 AC: 3233 AN: 3466

East Asian (EAS) AF: 0.885 AC: 4573 AN: 5168

South Asian (SAS) AF: 0.883 AC: 4254 AN: 4818

European-Finnish (FIN) AF: 0.871 AC: 9224 AN: 10592

Middle Eastern (MID) AF: 0.918 AC: 270 AN: 294

European-Non Finnish (NFE) AF: 0.855 AC: 58129 AN: 67976

Other (OTH) AF: 0.918 AC: 1938 AN: 2112

Alfa AF: 0.878 Hom.: 148096

Bravo AF: 0.903

Asia WGS AF: 0.901 AC: 3134 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.040
DANN	Benign	0.50
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs3129868; hg19: chr6-32404377;