rs3129860

Variant names:

• chr6-32433302-A-G
• rs3129860
• ENST00000766007.1:n.280-2571T>C

Your query was ambiguous. Multiple possible variants found:

• chr6-32433302-A-G
• chr6-32433302-A-T

Variant summary

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

The ENST00000766007.1(ENSG00000299747):​n.280-2571T>C 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 152,230 control chromosomes in the GnomAD database, including 60,951 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 (60951 hom., cov: 32)
• Consequence: ENSG00000299747 ENST00000766007.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.00
• Publications: 62 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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.944 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.280-2571T>C		intron_variant	Intron 2 of 2
ENSG00000299769	ENST00000766247.1	n.283-790A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.894 AC: 135949 AN: 152112 Hom.: 60897 Cov.: 32

Gnomad AFR AF: 0.952

Gnomad AMI AF: 0.913

Gnomad AMR AF: 0.918

Gnomad ASJ AF: 0.933

Gnomad EAS AF: 0.884

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: 136062 AN: 152230 Hom.: 60951 Cov.: 32 AF XY: 0.893 AC XY: 66471 AN XY: 74416

African (AFR) AF: 0.951 AC: 39529 AN: 41548

American (AMR) AF: 0.919 AC: 14039 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.933 AC: 3238 AN: 3472

East Asian (EAS) AF: 0.884 AC: 4586 AN: 5186

South Asian (SAS) AF: 0.883 AC: 4262 AN: 4828

European-Finnish (FIN) AF: 0.871 AC: 9217 AN: 10588

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

European-Non Finnish (NFE) AF: 0.855 AC: 58146 AN: 68004

Other (OTH) AF: 0.918 AC: 1942 AN: 2116

Alfa AF: 0.870 Hom.: 141871

Bravo AF: 0.903

Asia WGS AF: 0.904 AC: 3145 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.13
DANN	Benign	0.42
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs3129860; hg19: chr6-32401079;