rs996343

Variant names:

• chr7-145321424-A-G
• rs996343

Your query was ambiguous. Multiple possible variants found:

• chr7-145321424-A-G
• chr7-145321424-A-T

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 0.397 in 152,000 control chromosomes in the GnomAD database, including 13,010 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 (13010 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.583
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.767 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: 0.398 AC: 60390 AN: 151882 Hom.: 13013 Cov.: 33

Gnomad AFR AF: 0.281

Gnomad AMI AF: 0.369

Gnomad AMR AF: 0.417

Gnomad ASJ AF: 0.381

Gnomad EAS AF: 0.787

Gnomad SAS AF: 0.595

Gnomad FIN AF: 0.458

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.413

Gnomad OTH AF: 0.394

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

GnomAD4 genome AF: 0.397 AC: 60405 AN: 152000 Hom.: 13010 Cov.: 33 AF XY: 0.405 AC XY: 30102 AN XY: 74282

African (AFR) AF: 0.281 AC: 11649 AN: 41488

American (AMR) AF: 0.417 AC: 6364 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.381 AC: 1322 AN: 3470

East Asian (EAS) AF: 0.787 AC: 4063 AN: 5164

South Asian (SAS) AF: 0.595 AC: 2865 AN: 4816

European-Finnish (FIN) AF: 0.458 AC: 4830 AN: 10554

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.413 AC: 28027 AN: 67934

Other (OTH) AF: 0.396 AC: 835 AN: 2106

Alfa AF: 0.413 Hom.: 2346

Bravo AF: 0.390

Asia WGS AF: 0.680 AC: 2363 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.27
DANN	Benign	0.45
PhyloP100		-0.58

Splicing

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

Other links and lift over

dbSNP: rs996343; hg19: chr7-145018517;