chr7-143310018-G-A

Variant names:

• chr7-143310018-G-A
• rs7810486

Variant summary

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

The variant allele was found at a frequency of 0.396 in 152,050 control chromosomes in the GnomAD database, including 14,521 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 0.40 (14521 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.293
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.665 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.396 AC: 60131 AN: 151932 Hom.: 14478 Cov.: 32

Gnomad AFR AF: 0.672

Gnomad AMI AF: 0.420

Gnomad AMR AF: 0.298

Gnomad ASJ AF: 0.378

Gnomad EAS AF: 0.0439

Gnomad SAS AF: 0.294

Gnomad FIN AF: 0.197

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.314

Gnomad OTH AF: 0.411

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

GnomAD4 genome AF: 0.396 AC: 60221 AN: 152050 Hom.: 14521 Cov.: 32 AF XY: 0.385 AC XY: 28590 AN XY: 74336

African (AFR) AF: 0.672 AC: 27853 AN: 41452

American (AMR) AF: 0.298 AC: 4553 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.378 AC: 1312 AN: 3470

East Asian (EAS) AF: 0.0440 AC: 228 AN: 5184

South Asian (SAS) AF: 0.296 AC: 1423 AN: 4814

European-Finnish (FIN) AF: 0.197 AC: 2085 AN: 10562

Middle Eastern (MID) AF: 0.609 AC: 179 AN: 294

European-Non Finnish (NFE) AF: 0.314 AC: 21338 AN: 67962

Other (OTH) AF: 0.411 AC: 867 AN: 2112

Alfa AF: 0.336 Hom.: 4891

Bravo AF: 0.415

Asia WGS AF: 0.222 AC: 772 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.71
DANN	Benign	0.63
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs7810486; hg19: chr7-143007111;