7-68880612-G-A

Position:

• chr7-68880612-G-A

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 0.576 in 152,004 control chromosomes in the GnomAD database, including 25,559 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 0.58 (25559 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.54

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.651 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.577 AC: 87569 AN: 151888 Hom.: 25545 Cov.: 32

Gnomad AFR AF: 0.523

Gnomad AMI AF: 0.531

Gnomad AMR AF: 0.662

Gnomad ASJ AF: 0.563

Gnomad EAS AF: 0.607

Gnomad SAS AF: 0.557

Gnomad FIN AF: 0.586

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.589

Gnomad OTH AF: 0.585

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

GnomAD4 genome AF: 0.576 AC: 87627 AN: 152004 Hom.: 25559 Cov.: 32 AF XY: 0.577 AC XY: 42900 AN XY: 74288

Gnomad4 AFR AF: 0.523

Gnomad4 AMR AF: 0.662

Gnomad4 ASJ AF: 0.563

Gnomad4 EAS AF: 0.607

Gnomad4 SAS AF: 0.558

Gnomad4 FIN AF: 0.586

Gnomad4 NFE AF: 0.589

Gnomad4 OTH AF: 0.588

Alfa AF: 0.594 Hom.: 27006

Bravo AF: 0.581

Asia WGS AF: 0.564 AC: 1962 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.72
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10271980; hg19: chr7-68345599;