chr7-133231208-C-T

Variant names:

• chr7-133231208-C-T
• rs6951889

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 0.278 in 152,066 control chromosomes in the GnomAD database, including 6,993 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 0.28 (6993 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.794

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.458 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: 0.278 AC: 42190 AN: 151948 Hom.: 6978 Cov.: 32

Gnomad AFR AF: 0.463

Gnomad AMI AF: 0.147

Gnomad AMR AF: 0.198

Gnomad ASJ AF: 0.260

Gnomad EAS AF: 0.0547

Gnomad SAS AF: 0.178

Gnomad FIN AF: 0.192

Gnomad MID AF: 0.255

Gnomad NFE AF: 0.223

Gnomad OTH AF: 0.278

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

GnomAD4 genome AF: 0.278 AC: 42244 AN: 152066 Hom.: 6993 Cov.: 32 AF XY: 0.272 AC XY: 20208 AN XY: 74346

Gnomad4 AFR AF: 0.463

Gnomad4 AMR AF: 0.197

Gnomad4 ASJ AF: 0.260

Gnomad4 EAS AF: 0.0548

Gnomad4 SAS AF: 0.178

Gnomad4 FIN AF: 0.192

Gnomad4 NFE AF: 0.223

Gnomad4 OTH AF: 0.275

Alfa AF: 0.270 Hom.: 1142

Bravo AF: 0.286

Asia WGS AF: 0.125 AC: 435 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.4
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6951889; hg19: chr7-132915965;