7-121312528-C-A

Variant names:

• chr7-121312528-C-A
• rs10231005

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 0.422 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
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.566 AC: 23488 AN: 41482

American (AMR) AF: 0.360 AC: 5499 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.433 AC: 1504 AN: 3470

East Asian (EAS) AF: 0.414 AC: 2144 AN: 5176

South Asian (SAS) AF: 0.546 AC: 2631 AN: 4822

European-Finnish (FIN) AF: 0.287 AC: 3028 AN: 10560

Middle Eastern (MID) AF: 0.408 AC: 120 AN: 294

European-Non Finnish (NFE) AF: 0.362 AC: 24590 AN: 67950

Other (OTH) AF: 0.432 AC: 914 AN: 2116

Alfa AF: 0.383 Hom.: 36974

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
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs10231005; hg19: chr7-120952582;