chr9-1979764-T-C

Variant names:

• chr9-1979764-T-C
• rs1416621

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 0.43 in 152,120 control chromosomes in the GnomAD database, including 14,334 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 0.43 (14334 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.414
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.464 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.430 AC: 65307 AN: 152002 Hom.: 14327 Cov.: 33

Gnomad AFR AF: 0.469

Gnomad AMI AF: 0.222

Gnomad AMR AF: 0.406

Gnomad ASJ AF: 0.519

Gnomad EAS AF: 0.216

Gnomad SAS AF: 0.440

Gnomad FIN AF: 0.435

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.424

Gnomad OTH AF: 0.416

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

GnomAD4 genome AF: 0.430 AC: 65349 AN: 152120 Hom.: 14334 Cov.: 33 AF XY: 0.428 AC XY: 31841 AN XY: 74374

African (AFR) AF: 0.469 AC: 19459 AN: 41484

American (AMR) AF: 0.407 AC: 6224 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.519 AC: 1801 AN: 3468

East Asian (EAS) AF: 0.217 AC: 1124 AN: 5180

South Asian (SAS) AF: 0.438 AC: 2114 AN: 4826

European-Finnish (FIN) AF: 0.435 AC: 4597 AN: 10564

Middle Eastern (MID) AF: 0.486 AC: 142 AN: 292

European-Non Finnish (NFE) AF: 0.424 AC: 28815 AN: 67986

Other (OTH) AF: 0.413 AC: 871 AN: 2110

Alfa AF: 0.421 Hom.: 25401

Bravo AF: 0.427

Asia WGS AF: 0.321 AC: 1120 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	9.1
DANN	Benign	0.89
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs1416621; hg19: chr9-1979764; COSMIC: COSV71419213;