chr7-80741513-A-G

Variant names:

• chr7-80741513-A-G
• rs1527470

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 0.337 in 151,934 control chromosomes in the GnomAD database, including 9,961 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 0.34 (9961 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.299
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.443 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.338 AC: 51243 AN: 151816 Hom.: 9965 Cov.: 32

Gnomad AFR AF: 0.152

Gnomad AMI AF: 0.373

Gnomad AMR AF: 0.335

Gnomad ASJ AF: 0.471

Gnomad EAS AF: 0.0857

Gnomad SAS AF: 0.347

Gnomad FIN AF: 0.430

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.447

Gnomad OTH AF: 0.367

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

GnomAD4 genome AF: 0.337 AC: 51231 AN: 151934 Hom.: 9961 Cov.: 32 AF XY: 0.332 AC XY: 24679 AN XY: 74266

African (AFR) AF: 0.151 AC: 6276 AN: 41480

American (AMR) AF: 0.335 AC: 5104 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.471 AC: 1631 AN: 3466

East Asian (EAS) AF: 0.0857 AC: 444 AN: 5180

South Asian (SAS) AF: 0.347 AC: 1673 AN: 4824

European-Finnish (FIN) AF: 0.430 AC: 4527 AN: 10532

Middle Eastern (MID) AF: 0.395 AC: 116 AN: 294

European-Non Finnish (NFE) AF: 0.447 AC: 30354 AN: 67882

Other (OTH) AF: 0.363 AC: 766 AN: 2108

Alfa AF: 0.419 Hom.: 39911

Bravo AF: 0.323

Asia WGS AF: 0.204 AC: 709 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.9
DANN	Benign	0.73
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs1527470; hg19: chr7-80370829;