rs1880408

Variant names:

• chr7-42568038-A-G
• rs1880408

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 0.138 in 152,206 control chromosomes in the GnomAD database, including 2,853 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 0.14 (2853 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.582
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.348 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: 0.138 AC: 20975 AN: 152088 Hom.: 2848 Cov.: 32

Gnomad AFR AF: 0.353

Gnomad AMI AF: 0.155

Gnomad AMR AF: 0.0793

Gnomad ASJ AF: 0.0620

Gnomad EAS AF: 0.00578

Gnomad SAS AF: 0.0377

Gnomad FIN AF: 0.0305

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0584

Gnomad OTH AF: 0.127

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

GnomAD4 genome AF: 0.138 AC: 21020 AN: 152206 Hom.: 2853 Cov.: 32 AF XY: 0.132 AC XY: 9846 AN XY: 74416

African (AFR) AF: 0.353 AC: 14647 AN: 41474

American (AMR) AF: 0.0792 AC: 1211 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0620 AC: 215 AN: 3466

East Asian (EAS) AF: 0.00579 AC: 30 AN: 5182

South Asian (SAS) AF: 0.0375 AC: 181 AN: 4828

European-Finnish (FIN) AF: 0.0305 AC: 324 AN: 10620

Middle Eastern (MID) AF: 0.102 AC: 30 AN: 294

European-Non Finnish (NFE) AF: 0.0584 AC: 3971 AN: 68018

Other (OTH) AF: 0.128 AC: 270 AN: 2114

Alfa AF: 0.107 Hom.: 319

Bravo AF: 0.153

Asia WGS AF: 0.0560 AC: 194 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	5.5
DANN	Benign	0.73
PhyloP100		0.58

Splicing

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

Other links and lift over

dbSNP: rs1880408; hg19: chr7-42607637;