rs10231005

Positions:

• chr7-121312528-C-A
• chr7-121312528-C-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 0.422 in 152,052 control chromosomes in the GnomAD database, including 14,400 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 0.42 (14400 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.194

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.56 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.422 AC: 64078 AN: 151934 Hom.: 14383 Cov.: 33

Gnomad AFR AF: 0.566

Gnomad AMI AF: 0.247

Gnomad AMR AF: 0.361

Gnomad ASJ AF: 0.433

Gnomad EAS AF: 0.415

Gnomad SAS AF: 0.547

Gnomad FIN AF: 0.287

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.362

Gnomad OTH AF: 0.425

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

GnomAD4 genome AF: 0.422 AC: 64143 AN: 152052 Hom.: 14400 Cov.: 33 AF XY: 0.418 AC XY: 31045 AN XY: 74326

Gnomad4 AFR AF: 0.566

Gnomad4 AMR AF: 0.360

Gnomad4 ASJ AF: 0.433

Gnomad4 EAS AF: 0.414

Gnomad4 SAS AF: 0.546

Gnomad4 FIN AF: 0.287

Gnomad4 NFE AF: 0.362

Gnomad4 OTH AF: 0.432

Alfa AF: 0.378 Hom.: 13516

Bravo AF: 0.430

Asia WGS AF: 0.507 AC: 1761 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	0.78
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10231005; hg19: chr7-120952582;