rs9354308

Variant names:

• chr6-65855460-G-A
• rs9354308
• ENST00000800215.1:n.219-5690C>T

Your query was ambiguous. Multiple possible variants found:

• chr6-65855460-G-A
• chr6-65855460-G-C
• chr6-65855460-G-T

Variant summary

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

The ENST00000800215.1(ENSG00000304165):​n.219-5690C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.655 in 151,932 control chromosomes in the GnomAD database, including 32,833 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 0.65 (32833 hom., cov: 32)
• Consequence: ENSG00000304165 ENST00000800215.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0550
• Publications: 13 publications found

Genes affected

ENSG00000304165 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.847 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
ENSG00000304165	ENST00000800215.1	n.219-5690C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.654 AC: 99346 AN: 151812 Hom.: 32793 Cov.: 32

Gnomad AFR AF: 0.625

Gnomad AMI AF: 0.597

Gnomad AMR AF: 0.718

Gnomad ASJ AF: 0.696

Gnomad EAS AF: 0.868

Gnomad SAS AF: 0.792

Gnomad FIN AF: 0.646

Gnomad MID AF: 0.677

Gnomad NFE AF: 0.632

Gnomad OTH AF: 0.661

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

GnomAD4 genome AF: 0.655 AC: 99442 AN: 151932 Hom.: 32833 Cov.: 32 AF XY: 0.663 AC XY: 49232 AN XY: 74234

African (AFR) AF: 0.625 AC: 25898 AN: 41430

American (AMR) AF: 0.718 AC: 10933 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.696 AC: 2418 AN: 3472

East Asian (EAS) AF: 0.868 AC: 4483 AN: 5166

South Asian (SAS) AF: 0.791 AC: 3810 AN: 4814

European-Finnish (FIN) AF: 0.646 AC: 6805 AN: 10542

Middle Eastern (MID) AF: 0.667 AC: 196 AN: 294

European-Non Finnish (NFE) AF: 0.632 AC: 42954 AN: 67976

Other (OTH) AF: 0.664 AC: 1402 AN: 2110

Alfa AF: 0.648 Hom.: 63950

Bravo AF: 0.659

Asia WGS AF: 0.812 AC: 2821 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.89
DANN	Benign	0.52
PhyloP100		0.055

Splicing

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

Other links and lift over

dbSNP: rs9354308; hg19: chr6-66565353;