rs3135365

Variant names:

• chr6-32421478-C-A
• rs3135365
• ENST00000766247.1:n.282+7108C>A

Your query was ambiguous. Multiple possible variants found:

• chr6-32421478-C-A
• chr6-32421478-C-G

Variant summary

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

The ENST00000766247.1(ENSG00000299769):​n.282+7108C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.796 in 152,108 control chromosomes in the GnomAD database, including 48,308 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 0.80 (48308 hom., cov: 32)
• Consequence: ENSG00000299769 ENST00000766247.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.955
• Publications: 27 publications found

Genes affected

ENSG00000299769 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.825 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
ENSG00000299769	ENST00000766247.1	n.282+7108C>A		intron_variant	Intron 2 of 2
ENSG00000299769	ENST00000766248.1	n.287-3890C>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.796 AC: 120976 AN: 151990 Hom.: 48277 Cov.: 32

Gnomad AFR AF: 0.756

Gnomad AMI AF: 0.863

Gnomad AMR AF: 0.830

Gnomad ASJ AF: 0.870

Gnomad EAS AF: 0.845

Gnomad SAS AF: 0.787

Gnomad FIN AF: 0.867

Gnomad MID AF: 0.902

Gnomad NFE AF: 0.793

Gnomad OTH AF: 0.814

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

GnomAD4 genome AF: 0.796 AC: 121058 AN: 152108 Hom.: 48308 Cov.: 32 AF XY: 0.799 AC XY: 59418 AN XY: 74360

African (AFR) AF: 0.755 AC: 31329 AN: 41472

American (AMR) AF: 0.830 AC: 12687 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.870 AC: 3020 AN: 3470

East Asian (EAS) AF: 0.846 AC: 4379 AN: 5176

South Asian (SAS) AF: 0.788 AC: 3801 AN: 4822

European-Finnish (FIN) AF: 0.867 AC: 9181 AN: 10592

Middle Eastern (MID) AF: 0.895 AC: 263 AN: 294

European-Non Finnish (NFE) AF: 0.793 AC: 53890 AN: 67970

Other (OTH) AF: 0.815 AC: 1721 AN: 2112

Alfa AF: 0.796 Hom.: 134675

Bravo AF: 0.793

Asia WGS AF: 0.802 AC: 2793 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	6.8
DANN	Benign	0.44
PhyloP100		-0.95

Splicing

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

Other links and lift over

dbSNP: rs3135365; hg19: chr6-32389255;