chr7-145582394-T-A

Variant names:

• chr7-145582394-T-A
• rs1880184

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 0.454 in 151,934 control chromosomes in the GnomAD database, including 15,796 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 0.45 (15796 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0700
• Publications: 0 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 (SAS) allele frequency at 95% confidence interval = 0.54 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: 0.454 AC: 68900 AN: 151818 Hom.: 15777 Cov.: 31

Gnomad AFR AF: 0.390

Gnomad AMI AF: 0.370

Gnomad AMR AF: 0.459

Gnomad ASJ AF: 0.495

Gnomad EAS AF: 0.486

Gnomad SAS AF: 0.558

Gnomad FIN AF: 0.435

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.484

Gnomad OTH AF: 0.466

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

GnomAD4 genome AF: 0.454 AC: 68963 AN: 151934 Hom.: 15796 Cov.: 31 AF XY: 0.456 AC XY: 33825 AN XY: 74250

African (AFR) AF: 0.390 AC: 16146 AN: 41416

American (AMR) AF: 0.459 AC: 7009 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.495 AC: 1718 AN: 3472

East Asian (EAS) AF: 0.486 AC: 2506 AN: 5158

South Asian (SAS) AF: 0.557 AC: 2691 AN: 4828

European-Finnish (FIN) AF: 0.435 AC: 4584 AN: 10542

Middle Eastern (MID) AF: 0.445 AC: 130 AN: 292

European-Non Finnish (NFE) AF: 0.484 AC: 32861 AN: 67938

Other (OTH) AF: 0.466 AC: 981 AN: 2106

Alfa AF: 0.461 Hom.: 2021

Bravo AF: 0.448

Asia WGS AF: 0.532 AC: 1846 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.0
DANN	Benign	0.77
PhyloP100		-0.070

Splicing

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

Other links and lift over

dbSNP: rs1880184; hg19: chr7-145279487;