7-80969826-T-C

Position:

• chr7-80969826-T-C

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 0.455 in 152,008 control chromosomes in the GnomAD database, including 16,360 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 (16360 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.747

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.537 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: 0.455 AC: 69085 AN: 151888 Hom.: 16350 Cov.: 31

Gnomad AFR AF: 0.362

Gnomad AMI AF: 0.491

Gnomad AMR AF: 0.546

Gnomad ASJ AF: 0.572

Gnomad EAS AF: 0.229

Gnomad SAS AF: 0.515

Gnomad FIN AF: 0.411

Gnomad MID AF: 0.529

Gnomad NFE AF: 0.503

Gnomad OTH AF: 0.484

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

GnomAD4 genome AF: 0.455 AC: 69133 AN: 152008 Hom.: 16360 Cov.: 31 AF XY: 0.451 AC XY: 33493 AN XY: 74324

Gnomad4 AFR AF: 0.362

Gnomad4 AMR AF: 0.547

Gnomad4 ASJ AF: 0.572

Gnomad4 EAS AF: 0.229

Gnomad4 SAS AF: 0.515

Gnomad4 FIN AF: 0.411

Gnomad4 NFE AF: 0.503

Gnomad4 OTH AF: 0.484

Alfa AF: 0.502 Hom.: 39927

Bravo AF: 0.458

Asia WGS AF: 0.402 AC: 1397 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.3
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1358503; hg19: chr7-80599142;