rs9469007

Variant names:

• chr6-31441247-T-C
• rs9469007
• ENST00000673857.1:n.63-21876T>C

Variant summary

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

The ENST00000673857.1(ENSG00000288587):​n.63-21876T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.364 in 151,498 control chromosomes in the GnomAD database, including 10,628 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 0.36 (10628 hom., cov: 31)
• Consequence: ENSG00000288587 ENST00000673857.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.735
• Publications: 14 publications found

Genes affected

ENSG00000288587 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.444 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
ENSG00000288587	ENST00000673857.1	n.63-21876T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.364 AC: 55087 AN: 151384 Hom.: 10614 Cov.: 31

Gnomad AFR AF: 0.449

Gnomad AMI AF: 0.443

Gnomad AMR AF: 0.418

Gnomad ASJ AF: 0.493

Gnomad EAS AF: 0.321

Gnomad SAS AF: 0.326

Gnomad FIN AF: 0.372

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.296

Gnomad OTH AF: 0.385

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

GnomAD4 genome AF: 0.364 AC: 55154 AN: 151498 Hom.: 10628 Cov.: 31 AF XY: 0.368 AC XY: 27237 AN XY: 74044

African (AFR) AF: 0.449 AC: 18497 AN: 41158

American (AMR) AF: 0.418 AC: 6339 AN: 15166

Ashkenazi Jewish (ASJ) AF: 0.493 AC: 1708 AN: 3468

East Asian (EAS) AF: 0.321 AC: 1642 AN: 5120

South Asian (SAS) AF: 0.326 AC: 1565 AN: 4802

European-Finnish (FIN) AF: 0.372 AC: 3920 AN: 10550

Middle Eastern (MID) AF: 0.459 AC: 133 AN: 290

European-Non Finnish (NFE) AF: 0.296 AC: 20133 AN: 67934

Other (OTH) AF: 0.388 AC: 813 AN: 2098

Alfa AF: 0.332 Hom.: 8499

Bravo AF: 0.371

Asia WGS AF: 0.378 AC: 1311 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.5
DANN	Benign	0.27
PhyloP100		-0.73

Splicing

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

Other links and lift over

dbSNP: rs9469007; hg19: chr6-31409024;