9-21683806-T-C

Variant names:

• chr9-21683806-T-C
• rs1377197

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 0.162 in 152,168 control chromosomes in the GnomAD database, including 2,480 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 0.16 (2480 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.211
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.23 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: 0.162 AC: 24616 AN: 152050 Hom.: 2481 Cov.: 32

Gnomad AFR AF: 0.0488

Gnomad AMI AF: 0.218

Gnomad AMR AF: 0.189

Gnomad ASJ AF: 0.194

Gnomad EAS AF: 0.0123

Gnomad SAS AF: 0.158

Gnomad FIN AF: 0.171

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.233

Gnomad OTH AF: 0.165

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

GnomAD4 genome AF: 0.162 AC: 24615 AN: 152168 Hom.: 2480 Cov.: 32 AF XY: 0.159 AC XY: 11829 AN XY: 74378

African (AFR) AF: 0.0486 AC: 2020 AN: 41544

American (AMR) AF: 0.189 AC: 2888 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.194 AC: 674 AN: 3470

East Asian (EAS) AF: 0.0124 AC: 64 AN: 5176

South Asian (SAS) AF: 0.157 AC: 758 AN: 4814

European-Finnish (FIN) AF: 0.171 AC: 1804 AN: 10574

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.233 AC: 15827 AN: 67988

Other (OTH) AF: 0.163 AC: 345 AN: 2114

Alfa AF: 0.212 Hom.: 3933

Bravo AF: 0.154

Asia WGS AF: 0.106 AC: 368 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	7.4
DANN	Benign	0.59
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs1377197; hg19: chr9-21683805;