rs9805004

Variant names:

• chr12-121128067-C-T
• rs9805004
• XR_001749352.3:n.328-1226G>A

Variant summary

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

The XR_001749352.3(LOC105370032):​n.328-1226G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0991 in 152,196 control chromosomes in the GnomAD database, including 806 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 0.099 (806 hom., cov: 31)
• Consequence: LOC105370032 XR_001749352.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0380
• Publications: 6 publications found

Genes affected

LOC105370032 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.149 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105370032	XR_001749352.3	n.328-1226G>A		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0991 AC: 15072 AN: 152078 Hom.: 803 Cov.: 31

Gnomad AFR AF: 0.0748

Gnomad AMI AF: 0.159

Gnomad AMR AF: 0.0958

Gnomad ASJ AF: 0.0701

Gnomad EAS AF: 0.115

Gnomad SAS AF: 0.158

Gnomad FIN AF: 0.0816

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.112

Gnomad OTH AF: 0.110

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

GnomAD4 genome AF: 0.0991 AC: 15085 AN: 152196 Hom.: 806 Cov.: 31 AF XY: 0.0976 AC XY: 7260 AN XY: 74422

African (AFR) AF: 0.0747 AC: 3103 AN: 41530

American (AMR) AF: 0.0956 AC: 1461 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0701 AC: 243 AN: 3468

East Asian (EAS) AF: 0.115 AC: 596 AN: 5176

South Asian (SAS) AF: 0.159 AC: 765 AN: 4818

European-Finnish (FIN) AF: 0.0816 AC: 865 AN: 10606

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.113 AC: 7650 AN: 67992

Other (OTH) AF: 0.108 AC: 228 AN: 2112

Alfa AF: 0.106 Hom.: 706

Bravo AF: 0.0969

Asia WGS AF: 0.123 AC: 427 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.6
DANN	Benign	0.73
PhyloP100		0.038

Splicing

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

Other links and lift over

dbSNP: rs9805004; hg19: chr12-121565870;