rs3885423

Variant names:

• chr9-21075676-T-C
• rs3885423

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 152,106 control chromosomes in the GnomAD database, including 1,358 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 (1358 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.736
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.195 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: 0.128 AC: 19429 AN: 151988 Hom.: 1356 Cov.: 32

Gnomad AFR AF: 0.153

Gnomad AMI AF: 0.104

Gnomad AMR AF: 0.0855

Gnomad ASJ AF: 0.210

Gnomad EAS AF: 0.205

Gnomad SAS AF: 0.173

Gnomad FIN AF: 0.0547

Gnomad MID AF: 0.247

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: 19434 AN: 152106 Hom.: 1358 Cov.: 32 AF XY: 0.126 AC XY: 9344 AN XY: 74352

African (AFR) AF: 0.153 AC: 6348 AN: 41488

American (AMR) AF: 0.0854 AC: 1303 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.210 AC: 728 AN: 3470

East Asian (EAS) AF: 0.205 AC: 1057 AN: 5158

South Asian (SAS) AF: 0.172 AC: 831 AN: 4818

European-Finnish (FIN) AF: 0.0547 AC: 580 AN: 10600

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.120 AC: 8131 AN: 67994

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

Alfa AF: 0.128 Hom.: 676

Bravo AF: 0.131

Asia WGS AF: 0.208 AC: 726 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.6
DANN	Benign	0.43
PhyloP100		-0.74

Splicing

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

Other links and lift over

dbSNP: rs3885423; hg19: chr9-21075675; COSMIC: COSV66525666;