rs2270628

chr7-45909971-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 0.24 in 152,134 control chromosomes in the GnomAD database, including 4,884 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 0.24 (4884 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.409

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.362 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.240 AC: 36417 AN: 152016 Hom.: 4864 Cov.: 32

Gnomad AFR AF: 0.366

Gnomad AMI AF: 0.0813

Gnomad AMR AF: 0.164

Gnomad ASJ AF: 0.228

Gnomad EAS AF: 0.184

Gnomad SAS AF: 0.0945

Gnomad FIN AF: 0.234

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.199

Gnomad OTH AF: 0.217

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

GnomAD4 genome AF: 0.240 AC: 36478 AN: 152134 Hom.: 4884 Cov.: 32 AF XY: 0.236 AC XY: 17523 AN XY: 74362

Gnomad4 AFR AF: 0.367

Gnomad4 AMR AF: 0.165

Gnomad4 ASJ AF: 0.228

Gnomad4 EAS AF: 0.183

Gnomad4 SAS AF: 0.0940

Gnomad4 FIN AF: 0.234

Gnomad4 NFE AF: 0.199

Gnomad4 OTH AF: 0.216

Alfa AF: 0.203 Hom.: 6502

Bravo AF: 0.245

Asia WGS AF: 0.141 AC: 492 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	2.2
Dann	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2270628; hg19: chr7-45949570;