7-45895920-C-T

Position:

• chr7-45895920-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 0.319 in 152,010 control chromosomes in the GnomAD database, including 7,904 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 0.32 (7904 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.52

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.31 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: 0.319 AC: 48512 AN: 151892 Hom.: 7887 Cov.: 32

Gnomad AFR AF: 0.312

Gnomad AMI AF: 0.395

Gnomad AMR AF: 0.301

Gnomad ASJ AF: 0.300

Gnomad EAS AF: 0.315

Gnomad SAS AF: 0.323

Gnomad FIN AF: 0.477

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.304

Gnomad OTH AF: 0.307

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

GnomAD4 genome AF: 0.319 AC: 48555 AN: 152010 Hom.: 7904 Cov.: 32 AF XY: 0.327 AC XY: 24291 AN XY: 74300

Gnomad4 AFR AF: 0.312

Gnomad4 AMR AF: 0.301

Gnomad4 ASJ AF: 0.300

Gnomad4 EAS AF: 0.316

Gnomad4 SAS AF: 0.323

Gnomad4 FIN AF: 0.477

Gnomad4 NFE AF: 0.304

Gnomad4 OTH AF: 0.304

Alfa AF: 0.321 Hom.: 1821

Bravo AF: 0.303

Asia WGS AF: 0.324 AC: 1125 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.70
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1908751; hg19: chr7-45935519;