rs9501129

Variant names:

• chr6-31449619-T-C
• rs9501129
• ENST00000673857.1:n.63-13504T>C

Your query was ambiguous. Multiple possible variants found:

• chr6-31449619-T-C
• chr6-31449619-T-G

Variant summary

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

The ENST00000673857.1(ENSG00000288587):​n.63-13504T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.214 in 151,546 control chromosomes in the GnomAD database, including 4,146 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 0.21 (4146 hom., cov: 31)
• Consequence: ENSG00000288587 ENST00000673857.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.375
• Publications: 13 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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.286 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.63-13504T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.214 AC: 32411 AN: 151428 Hom.: 4131 Cov.: 31

Gnomad AFR AF: 0.290

Gnomad AMI AF: 0.202

Gnomad AMR AF: 0.280

Gnomad ASJ AF: 0.280

Gnomad EAS AF: 0.252

Gnomad SAS AF: 0.222

Gnomad FIN AF: 0.246

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.141

Gnomad OTH AF: 0.222

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

GnomAD4 genome AF: 0.214 AC: 32476 AN: 151546 Hom.: 4146 Cov.: 31 AF XY: 0.220 AC XY: 16295 AN XY: 74068

African (AFR) AF: 0.290 AC: 11945 AN: 41170

American (AMR) AF: 0.281 AC: 4258 AN: 15162

Ashkenazi Jewish (ASJ) AF: 0.280 AC: 972 AN: 3470

East Asian (EAS) AF: 0.252 AC: 1299 AN: 5146

South Asian (SAS) AF: 0.222 AC: 1069 AN: 4808

European-Finnish (FIN) AF: 0.246 AC: 2586 AN: 10510

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.141 AC: 9611 AN: 67974

Other (OTH) AF: 0.226 AC: 475 AN: 2102

Alfa AF: 0.174 Hom.: 4692

Bravo AF: 0.219

Asia WGS AF: 0.240 AC: 832 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	5.4
DANN	Benign	0.72
PhyloP100		-0.38

Splicing

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

Other links and lift over

dbSNP: rs9501129; hg19: chr6-31417396;