chr9-21187929-T-C

Variant names:

• chr9-21187929-T-C
• rs7870840

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 0.343 in 152,040 control chromosomes in the GnomAD database, including 9,980 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 0.34 (9980 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0180
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.432 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: 0.343 AC: 52077 AN: 151922 Hom.: 9981 Cov.: 33

Gnomad AFR AF: 0.181

Gnomad AMI AF: 0.397

Gnomad AMR AF: 0.344

Gnomad ASJ AF: 0.441

Gnomad EAS AF: 0.150

Gnomad SAS AF: 0.292

Gnomad FIN AF: 0.451

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.436

Gnomad OTH AF: 0.356

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

GnomAD4 genome AF: 0.343 AC: 52079 AN: 152040 Hom.: 9980 Cov.: 33 AF XY: 0.342 AC XY: 25442 AN XY: 74334

African (AFR) AF: 0.181 AC: 7514 AN: 41512

American (AMR) AF: 0.345 AC: 5262 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.441 AC: 1532 AN: 3470

East Asian (EAS) AF: 0.150 AC: 777 AN: 5188

South Asian (SAS) AF: 0.292 AC: 1406 AN: 4820

European-Finnish (FIN) AF: 0.451 AC: 4752 AN: 10542

Middle Eastern (MID) AF: 0.401 AC: 118 AN: 294

European-Non Finnish (NFE) AF: 0.436 AC: 29615 AN: 67928

Other (OTH) AF: 0.351 AC: 741 AN: 2112

Alfa AF: 0.377 Hom.: 1386

Bravo AF: 0.327

Asia WGS AF: 0.203 AC: 699 AN: 3436

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.0
DANN	Benign	0.77
PhyloP100		0.018
PromoterAI		-0.0029	Neutral

Splicing

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

Other links and lift over

dbSNP: rs7870840; hg19: chr9-21187928; COSMIC: COSV70179758;