7-45922864-T-G

Variant names:

• chr7-45922864-T-G
• rs2132570

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.784 in 151,984 control chromosomes in the GnomAD database, including 47,306 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 0.78 (47306 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.110
• Publications: 22 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.873 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: 0.784 AC: 119011 AN: 151866 Hom.: 47268 Cov.: 31

Gnomad AFR AF: 0.880

Gnomad AMI AF: 0.838

Gnomad AMR AF: 0.622

Gnomad ASJ AF: 0.868

Gnomad EAS AF: 0.786

Gnomad SAS AF: 0.779

Gnomad FIN AF: 0.635

Gnomad MID AF: 0.861

Gnomad NFE AF: 0.779

Gnomad OTH AF: 0.792

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

GnomAD4 genome AF: 0.784 AC: 119099 AN: 151984 Hom.: 47306 Cov.: 31 AF XY: 0.775 AC XY: 57532 AN XY: 74262

African (AFR) AF: 0.880 AC: 36515 AN: 41488

American (AMR) AF: 0.621 AC: 9467 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.868 AC: 3012 AN: 3472

East Asian (EAS) AF: 0.787 AC: 4065 AN: 5168

South Asian (SAS) AF: 0.779 AC: 3748 AN: 4812

European-Finnish (FIN) AF: 0.635 AC: 6689 AN: 10526

Middle Eastern (MID) AF: 0.864 AC: 254 AN: 294

European-Non Finnish (NFE) AF: 0.779 AC: 52914 AN: 67964

Other (OTH) AF: 0.795 AC: 1672 AN: 2104

Alfa AF: 0.789 Hom.: 10642

Bravo AF: 0.784

Asia WGS AF: 0.768 AC: 2673 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.9
DANN	Benign	0.41
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs2132570; hg19: chr7-45962463;