rs7042864

Variant names:

• chr9-108110027-C-T
• rs7042864
• XR_001746881.2:n.721-56733G>A

Variant summary

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

The XR_001746881.2(LOC105376214):​n.721-56733G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.319 in 152,034 control chromosomes in the GnomAD database, including 8,082 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 0.32 (8082 hom., cov: 32)
• Consequence: LOC105376214 XR_001746881.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.12
• Publications: 9 publications found

Genes affected

LOC105376214 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.352 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.319 AC: 48451 AN: 151916 Hom.: 8082 Cov.: 32

Gnomad AFR AF: 0.291

Gnomad AMI AF: 0.619

Gnomad AMR AF: 0.303

Gnomad ASJ AF: 0.254

Gnomad EAS AF: 0.0684

Gnomad SAS AF: 0.358

Gnomad FIN AF: 0.312

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.355

Gnomad OTH AF: 0.347

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

GnomAD4 genome AF: 0.319 AC: 48470 AN: 152034 Hom.: 8082 Cov.: 32 AF XY: 0.315 AC XY: 23384 AN XY: 74290

African (AFR) AF: 0.291 AC: 12052 AN: 41478

American (AMR) AF: 0.302 AC: 4621 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.254 AC: 881 AN: 3470

East Asian (EAS) AF: 0.0682 AC: 352 AN: 5160

South Asian (SAS) AF: 0.357 AC: 1718 AN: 4806

European-Finnish (FIN) AF: 0.312 AC: 3298 AN: 10558

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.355 AC: 24159 AN: 67968

Other (OTH) AF: 0.343 AC: 724 AN: 2110

Alfa AF: 0.335 Hom.: 33220

Bravo AF: 0.314

Asia WGS AF: 0.231 AC: 804 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	11
DANN	Benign	0.56
PhyloP100		2.1

Splicing

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

Other links and lift over

dbSNP: rs7042864; hg19: chr9-110872307;