7-68889544-C-T

Position:

• chr7-68889544-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 0.635 in 151,854 control chromosomes in the GnomAD database, including 30,844 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 0.64 (30844 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0620

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.721 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: 0.635 AC: 96375 AN: 151736 Hom.: 30816 Cov.: 31

Gnomad AFR AF: 0.639

Gnomad AMI AF: 0.590

Gnomad AMR AF: 0.732

Gnomad ASJ AF: 0.550

Gnomad EAS AF: 0.683

Gnomad SAS AF: 0.577

Gnomad FIN AF: 0.646

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.615

Gnomad OTH AF: 0.640

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

GnomAD4 genome AF: 0.635 AC: 96452 AN: 151854 Hom.: 30844 Cov.: 31 AF XY: 0.638 AC XY: 47318 AN XY: 74180

Gnomad4 AFR AF: 0.639

Gnomad4 AMR AF: 0.732

Gnomad4 ASJ AF: 0.550

Gnomad4 EAS AF: 0.682

Gnomad4 SAS AF: 0.577

Gnomad4 FIN AF: 0.646

Gnomad4 NFE AF: 0.615

Gnomad4 OTH AF: 0.643

Alfa AF: 0.625 Hom.: 3574

Bravo AF: 0.644

Asia WGS AF: 0.651 AC: 2263 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.0
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4718827; hg19: chr7-68354531;