rs1416621

Variant names:

• chr9-1979764-T-C
• rs1416621

Your query was ambiguous. Multiple possible variants found:

• chr9-1979764-T-C
• chr9-1979764-T-G

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.430 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

Gnomad4 AFR AF: 0.469

Gnomad4 AMR AF: 0.407

Gnomad4 ASJ AF: 0.519

Gnomad4 EAS AF: 0.217

Gnomad4 SAS AF: 0.438

Gnomad4 FIN AF: 0.435

Gnomad4 NFE AF: 0.424

Gnomad4 OTH AF: 0.413

Alfa AF: 0.418 Hom.: 18178

Bravo AF: 0.427

Asia WGS AF: 0.321 AC: 1120 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

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