rs7873167

Variant names:

• chr9-21075445-T-G
• rs7873167

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 0.128 in 152,194 control chromosomes in the GnomAD database, including 1,347 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 0.13 (1347 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.585
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.189 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.128 AC: 19422 AN: 152076 Hom.: 1345 Cov.: 32

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.102

Gnomad AMR AF: 0.0855

Gnomad ASJ AF: 0.210

Gnomad EAS AF: 0.200

Gnomad SAS AF: 0.172

Gnomad FIN AF: 0.0547

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.120

Gnomad OTH AF: 0.135

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

GnomAD4 genome AF: 0.128 AC: 19427 AN: 152194 Hom.: 1347 Cov.: 32 AF XY: 0.126 AC XY: 9340 AN XY: 74412

African (AFR) AF: 0.153 AC: 6367 AN: 41504

American (AMR) AF: 0.0854 AC: 1305 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.210 AC: 730 AN: 3468

East Asian (EAS) AF: 0.199 AC: 1032 AN: 5178

South Asian (SAS) AF: 0.172 AC: 830 AN: 4826

European-Finnish (FIN) AF: 0.0547 AC: 581 AN: 10616

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.120 AC: 8127 AN: 68000

Other (OTH) AF: 0.138 AC: 293 AN: 2116

Alfa AF: 0.116 Hom.: 437

Bravo AF: 0.131

Asia WGS AF: 0.203 AC: 707 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	2.0
DANN	Benign	0.55
PhyloP100		-0.58

Splicing

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

Other links and lift over

dbSNP: rs7873167; hg19: chr9-21075444; COSMIC: COSV66525662;