rs9356206

Variant names:

• chr6-164397801-G-A
• rs9356206
• ENST00000850290.1:n.778-39886G>A

Variant summary

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

The ENST00000850290.1(ENSG00000310478):​n.778-39886G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0797 in 152,182 control chromosomes in the GnomAD database, including 652 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 0.080 (652 hom., cov: 32)
• Consequence: ENSG00000310478 ENST00000850290.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.582
• Publications: 2 publications found

Genes affected

ENSG00000310478 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.134 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
ENSG00000310478	ENST00000850290.1	n.778-39886G>A		intron_variant	Intron 1 of 1
ENSG00000310478	ENST00000850291.1	n.714-39886G>A		intron_variant	Intron 1 of 1
ENSG00000310478	ENST00000850292.1	n.763-10438G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0796 AC: 12100 AN: 152064 Hom.: 649 Cov.: 32

Gnomad AFR AF: 0.137

Gnomad AMI AF: 0.0835

Gnomad AMR AF: 0.0569

Gnomad ASJ AF: 0.0392

Gnomad EAS AF: 0.0943

Gnomad SAS AF: 0.0774

Gnomad FIN AF: 0.0230

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0601

Gnomad OTH AF: 0.0670

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

GnomAD4 genome AF: 0.0797 AC: 12124 AN: 152182 Hom.: 652 Cov.: 32 AF XY: 0.0785 AC XY: 5843 AN XY: 74420

African (AFR) AF: 0.137 AC: 5692 AN: 41506

American (AMR) AF: 0.0568 AC: 870 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0392 AC: 136 AN: 3468

East Asian (EAS) AF: 0.0943 AC: 488 AN: 5174

South Asian (SAS) AF: 0.0770 AC: 371 AN: 4818

European-Finnish (FIN) AF: 0.0230 AC: 244 AN: 10596

Middle Eastern (MID) AF: 0.0544 AC: 16 AN: 294

European-Non Finnish (NFE) AF: 0.0601 AC: 4089 AN: 68000

Other (OTH) AF: 0.0672 AC: 142 AN: 2112

Alfa AF: 0.0653 Hom.: 615

Bravo AF: 0.0838

Asia WGS AF: 0.117 AC: 406 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.93
DANN	Benign	0.58
PhyloP100		-0.58

Splicing

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

Other links and lift over

dbSNP: rs9356206; hg19: chr6-164818834;