7-80741513-A-G

Position:

• chr7-80741513-A-G

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 0.337 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

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

Gnomad4 AFR AF: 0.151

Gnomad4 AMR AF: 0.335

Gnomad4 ASJ AF: 0.471

Gnomad4 EAS AF: 0.0857

Gnomad4 SAS AF: 0.347

Gnomad4 FIN AF: 0.430

Gnomad4 NFE AF: 0.447

Gnomad4 OTH AF: 0.363

Alfa AF: 0.426 Hom.: 27951

Bravo AF: 0.323

Asia WGS AF: 0.204 AC: 709 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1527470; hg19: chr7-80370829;