rs3129871

Variant names:

• chr6-32438565-A-C
• rs3129871
• ENST00000766007.1:n.163-305T>G

Your query was ambiguous. Multiple possible variants found:

• chr6-32438565-A-C
• chr6-32438565-A-G
• chr6-32438565-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.163-305T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.593 in 152,088 control chromosomes in the GnomAD database, including 27,309 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 0.59 (27309 hom., cov: 32)
• Consequence: ENSG00000299747 ENST00000766007.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.37
• Publications: 84 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 (EAS) allele frequency at 95% confidence interval = 0.672 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.163-305T>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.593 AC: 90106 AN: 151970 Hom.: 27303 Cov.: 32

Gnomad AFR AF: 0.449

Gnomad AMI AF: 0.677

Gnomad AMR AF: 0.633

Gnomad ASJ AF: 0.662

Gnomad EAS AF: 0.691

Gnomad SAS AF: 0.655

Gnomad FIN AF: 0.640

Gnomad MID AF: 0.715

Gnomad NFE AF: 0.647

Gnomad OTH AF: 0.603

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

GnomAD4 genome AF: 0.593 AC: 90140 AN: 152088 Hom.: 27309 Cov.: 32 AF XY: 0.596 AC XY: 44332 AN XY: 74342

African (AFR) AF: 0.449 AC: 18617 AN: 41482

American (AMR) AF: 0.633 AC: 9672 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.662 AC: 2298 AN: 3472

East Asian (EAS) AF: 0.691 AC: 3565 AN: 5158

South Asian (SAS) AF: 0.657 AC: 3170 AN: 4826

European-Finnish (FIN) AF: 0.640 AC: 6761 AN: 10560

Middle Eastern (MID) AF: 0.704 AC: 207 AN: 294

European-Non Finnish (NFE) AF: 0.647 AC: 43954 AN: 67978

Other (OTH) AF: 0.604 AC: 1279 AN: 2116

Alfa AF: 0.647 Hom.: 120430

Bravo AF: 0.585

Asia WGS AF: 0.649 AC: 2261 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	0.094
DANN	Benign	0.19
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs3129871; hg19: chr6-32406342;