7-12210267-C-T

Position:

• chr7-12210267-C-T

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 0.761 in 152,150 control chromosomes in the GnomAD database, including 44,916 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 0.76 (44916 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.58

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.929 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: 0.760 AC: 115611 AN: 152030 Hom.: 44862 Cov.: 32

Gnomad AFR AF: 0.937

Gnomad AMI AF: 0.652

Gnomad AMR AF: 0.738

Gnomad ASJ AF: 0.709

Gnomad EAS AF: 0.680

Gnomad SAS AF: 0.730

Gnomad FIN AF: 0.695

Gnomad MID AF: 0.720

Gnomad NFE AF: 0.681

Gnomad OTH AF: 0.737

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

GnomAD4 genome AF: 0.761 AC: 115720 AN: 152150 Hom.: 44916 Cov.: 32 AF XY: 0.760 AC XY: 56521 AN XY: 74370

Gnomad4 AFR AF: 0.937

Gnomad4 AMR AF: 0.738

Gnomad4 ASJ AF: 0.709

Gnomad4 EAS AF: 0.680

Gnomad4 SAS AF: 0.728

Gnomad4 FIN AF: 0.695

Gnomad4 NFE AF: 0.681

Gnomad4 OTH AF: 0.736

Alfa AF: 0.697 Hom.: 49590

Bravo AF: 0.771

Asia WGS AF: 0.727 AC: 2526 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.093
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1435528; hg19: chr7-12249893;