rs9320913

Variant names:

• chr6-98136857-C-A
• rs9320913
• ENST00000606913.5:n.240+37587C>A

Variant summary

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

The ENST00000606913.5(ENSG00000271860):​n.240+37587C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.384 in 148,960 control chromosomes in the GnomAD database, including 11,815 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 0.38 (11815 hom., cov: 31)
• Consequence: ENSG00000271860 ENST00000606913.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.801
• Publications: 34 publications found

Genes affected

ENSG00000271860 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.475 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
ENSG00000271860	ENST00000606913.5	n.240+37587C>A		intron_variant	Intron 2 of 4	5
ENSG00000271860	ENST00000607032.1	n.410+37587C>A		intron_variant	Intron 4 of 7	3
ENSG00000271860	ENST00000607823.5	n.352+37587C>A		intron_variant	Intron 4 of 6	5

Frequencies

GnomAD3 genomes AF: 0.384 AC: 57219 AN: 148856 Hom.: 11819 Cov.: 31

Gnomad AFR AF: 0.218

Gnomad AMI AF: 0.442

Gnomad AMR AF: 0.346

Gnomad ASJ AF: 0.479

Gnomad EAS AF: 0.396

Gnomad SAS AF: 0.256

Gnomad FIN AF: 0.483

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.480

Gnomad OTH AF: 0.393

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

GnomAD4 genome AF: 0.384 AC: 57208 AN: 148960 Hom.: 11815 Cov.: 31 AF XY: 0.381 AC XY: 27726 AN XY: 72688

African (AFR) AF: 0.218 AC: 8810 AN: 40488

American (AMR) AF: 0.346 AC: 5187 AN: 15004

Ashkenazi Jewish (ASJ) AF: 0.479 AC: 1649 AN: 3444

East Asian (EAS) AF: 0.396 AC: 2003 AN: 5062

South Asian (SAS) AF: 0.257 AC: 1189 AN: 4628

European-Finnish (FIN) AF: 0.483 AC: 4904 AN: 10160

Middle Eastern (MID) AF: 0.541 AC: 146 AN: 270

European-Non Finnish (NFE) AF: 0.480 AC: 32123 AN: 66942

Other (OTH) AF: 0.387 AC: 799 AN: 2062

Alfa AF: 0.262 Hom.: 1759

Bravo AF: 0.371

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.37
DANN	Benign	0.20
PhyloP100		-0.80

Splicing

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

Other links and lift over

dbSNP: rs9320913; hg19: chr6-98584733;