chr7-145499433-T-C

Variant names:

• chr7-145499433-T-C
• rs20451

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 0.121 in 152,228 control chromosomes in the GnomAD database, including 3,063 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 0.12 (3063 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.10

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.374 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: 0.120 AC: 18312 AN: 152110 Hom.: 3054 Cov.: 33

Gnomad AFR AF: 0.378

Gnomad AMI AF: 0.00877

Gnomad AMR AF: 0.0431

Gnomad ASJ AF: 0.0838

Gnomad EAS AF: 0.0553

Gnomad SAS AF: 0.0313

Gnomad FIN AF: 0.00386

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0148

Gnomad OTH AF: 0.0964

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

GnomAD4 genome AF: 0.121 AC: 18360 AN: 152228 Hom.: 3063 Cov.: 33 AF XY: 0.117 AC XY: 8681 AN XY: 74424

Gnomad4 AFR AF: 0.379

Gnomad4 AMR AF: 0.0429

Gnomad4 ASJ AF: 0.0838

Gnomad4 EAS AF: 0.0552

Gnomad4 SAS AF: 0.0303

Gnomad4 FIN AF: 0.00386

Gnomad4 NFE AF: 0.0148

Gnomad4 OTH AF: 0.0954

Alfa AF: 0.0799 Hom.: 243

Bravo AF: 0.136

Asia WGS AF: 0.0610 AC: 213 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.85
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs20451; hg19: chr7-145196526;