7-45939968-T-G

Position:

• chr7-45939968-T-G

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 0.171 in 152,226 control chromosomes in the GnomAD database, including 2,393 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 0.17 (2393 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.282 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: 0.171 AC: 25998 AN: 152108 Hom.: 2389 Cov.: 32

Gnomad AFR AF: 0.140

Gnomad AMI AF: 0.152

Gnomad AMR AF: 0.167

Gnomad ASJ AF: 0.248

Gnomad EAS AF: 0.0330

Gnomad SAS AF: 0.293

Gnomad FIN AF: 0.127

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.194

Gnomad OTH AF: 0.207

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

GnomAD4 genome AF: 0.171 AC: 26024 AN: 152226 Hom.: 2393 Cov.: 32 AF XY: 0.169 AC XY: 12588 AN XY: 74430

Gnomad4 AFR AF: 0.140

Gnomad4 AMR AF: 0.167

Gnomad4 ASJ AF: 0.248

Gnomad4 EAS AF: 0.0330

Gnomad4 SAS AF: 0.294

Gnomad4 FIN AF: 0.127

Gnomad4 NFE AF: 0.194

Gnomad4 OTH AF: 0.213

Alfa AF: 0.190 Hom.: 585

Bravo AF: 0.169

Asia WGS AF: 0.196 AC: 682 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.7
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2471554; hg19: chr7-45979567;