7-80233787-C-T

Position:

• chr7-80233787-C-T

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 0.537 in 152,036 control chromosomes in the GnomAD database, including 25,955 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 0.54 (25955 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.30

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.86 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: 0.537 AC: 81562 AN: 151916 Hom.: 25944 Cov.: 32

Gnomad AFR AF: 0.176

Gnomad AMI AF: 0.686

Gnomad AMR AF: 0.618

Gnomad ASJ AF: 0.697

Gnomad EAS AF: 0.881

Gnomad SAS AF: 0.645

Gnomad FIN AF: 0.693

Gnomad MID AF: 0.587

Gnomad NFE AF: 0.668

Gnomad OTH AF: 0.587

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

GnomAD4 genome AF: 0.537 AC: 81583 AN: 152036 Hom.: 25955 Cov.: 32 AF XY: 0.542 AC XY: 40279 AN XY: 74318

Gnomad4 AFR AF: 0.176

Gnomad4 AMR AF: 0.619

Gnomad4 ASJ AF: 0.697

Gnomad4 EAS AF: 0.881

Gnomad4 SAS AF: 0.645

Gnomad4 FIN AF: 0.693

Gnomad4 NFE AF: 0.668

Gnomad4 OTH AF: 0.592

Alfa AF: 0.620 Hom.: 13489

Bravo AF: 0.518

Asia WGS AF: 0.725 AC: 2519 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.49
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4731302; hg19: chr7-79863103;