rs10488055

Variant names:

• chr7-121801926-T-A
• rs10488055

Your query was ambiguous. Multiple possible variants found:

• chr7-121801926-T-A
• chr7-121801926-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 0.319 in 151,964 control chromosomes in the GnomAD database, including 7,904 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 0.32 (7904 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.411

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.371 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: 0.319 AC: 48380 AN: 151846 Hom.: 7896 Cov.: 31

Gnomad AFR AF: 0.290

Gnomad AMI AF: 0.220

Gnomad AMR AF: 0.264

Gnomad ASJ AF: 0.291

Gnomad EAS AF: 0.316

Gnomad SAS AF: 0.386

Gnomad FIN AF: 0.372

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.340

Gnomad OTH AF: 0.279

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

GnomAD4 genome AF: 0.319 AC: 48442 AN: 151964 Hom.: 7904 Cov.: 31 AF XY: 0.323 AC XY: 24001 AN XY: 74282

Gnomad4 AFR AF: 0.291

Gnomad4 AMR AF: 0.264

Gnomad4 ASJ AF: 0.291

Gnomad4 EAS AF: 0.317

Gnomad4 SAS AF: 0.386

Gnomad4 FIN AF: 0.372

Gnomad4 NFE AF: 0.340

Gnomad4 OTH AF: 0.278

Alfa AF: 0.337 Hom.: 1123

Bravo AF: 0.301

Asia WGS AF: 0.347 AC: 1207 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.6
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10488055; hg19: chr7-121441980;