rs7873404

Variant names:

• chr9-21228498-T-C
• rs7873404

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 0.279 in 152,008 control chromosomes in the GnomAD database, including 6,492 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 0.28 (6492 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0860
• Publications: 4 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 (EAS) allele frequency at 95% confidence interval = 0.501 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.278 AC: 42287 AN: 151890 Hom.: 6482 Cov.: 32

Gnomad AFR AF: 0.375

Gnomad AMI AF: 0.168

Gnomad AMR AF: 0.310

Gnomad ASJ AF: 0.241

Gnomad EAS AF: 0.518

Gnomad SAS AF: 0.193

Gnomad FIN AF: 0.209

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.215

Gnomad OTH AF: 0.269

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

GnomAD4 genome AF: 0.279 AC: 42340 AN: 152008 Hom.: 6492 Cov.: 32 AF XY: 0.278 AC XY: 20649 AN XY: 74294

African (AFR) AF: 0.375 AC: 15556 AN: 41460

American (AMR) AF: 0.310 AC: 4738 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.241 AC: 833 AN: 3458

East Asian (EAS) AF: 0.518 AC: 2672 AN: 5162

South Asian (SAS) AF: 0.195 AC: 939 AN: 4824

European-Finnish (FIN) AF: 0.209 AC: 2204 AN: 10570

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.215 AC: 14609 AN: 67956

Other (OTH) AF: 0.268 AC: 566 AN: 2110

Alfa AF: 0.257 Hom.: 702

Bravo AF: 0.294

Asia WGS AF: 0.338 AC: 1171 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.44
DANN	Benign	0.33
PhyloP100		0.086
PromoterAI		-0.0048	Neutral

Splicing

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

Other links and lift over

dbSNP: rs7873404; hg19: chr9-21228497;