rs9988960

Variant names:

• chr12-27819417-G-A
• rs9988960
• ENST00000825469.1:n.320+8327G>A

Your query was ambiguous. Multiple possible variants found:

• chr12-27819417-G-A
• chr12-27819417-G-T

Variant summary

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

The ENST00000825469.1(ENSG00000257042):​n.320+8327G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.388 in 152,008 control chromosomes in the GnomAD database, including 11,539 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 0.39 (11539 hom., cov: 32)
• Consequence: ENSG00000257042 ENST00000825469.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0900
• Publications: 8 publications found

Genes affected

ENSG00000257042 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.441 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105369709	XR_931459.3	n.245+1371C>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000257042	ENST00000825469.1	n.320+8327G>A		intron_variant	Intron 1 of 2
ENSG00000257042	ENST00000825470.1	n.175+8327G>A		intron_variant	Intron 1 of 2
ENSG00000257042	ENST00000825471.1	n.140+8327G>A		intron_variant	Intron 1 of 1
ENSG00000307385	ENST00000825567.1	n.253+1371C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.388 AC: 58933 AN: 151892 Hom.: 11540 Cov.: 32

Gnomad AFR AF: 0.391

Gnomad AMI AF: 0.370

Gnomad AMR AF: 0.349

Gnomad ASJ AF: 0.412

Gnomad EAS AF: 0.298

Gnomad SAS AF: 0.458

Gnomad FIN AF: 0.376

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.397

Gnomad OTH AF: 0.384

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

GnomAD4 genome AF: 0.388 AC: 58964 AN: 152008 Hom.: 11539 Cov.: 32 AF XY: 0.388 AC XY: 28818 AN XY: 74280

African (AFR) AF: 0.391 AC: 16221 AN: 41472

American (AMR) AF: 0.349 AC: 5334 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.412 AC: 1430 AN: 3468

East Asian (EAS) AF: 0.297 AC: 1530 AN: 5150

South Asian (SAS) AF: 0.457 AC: 2198 AN: 4808

European-Finnish (FIN) AF: 0.376 AC: 3958 AN: 10528

Middle Eastern (MID) AF: 0.480 AC: 141 AN: 294

European-Non Finnish (NFE) AF: 0.397 AC: 27016 AN: 67992

Other (OTH) AF: 0.379 AC: 799 AN: 2110

Alfa AF: 0.388 Hom.: 49952

Bravo AF: 0.380

Asia WGS AF: 0.398 AC: 1384 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.1
DANN	Benign	0.34
PhyloP100		-0.090

Splicing

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

Other links and lift over

dbSNP: rs9988960; hg19: chr12-27972350;