chr7-68889544-C-T

Variant names:

• chr7-68889544-C-T
• rs4718827

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.639 AC: 26450 AN: 41420

American (AMR) AF: 0.732 AC: 11185 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.550 AC: 1907 AN: 3470

East Asian (EAS) AF: 0.682 AC: 3497 AN: 5124

South Asian (SAS) AF: 0.577 AC: 2770 AN: 4798

European-Finnish (FIN) AF: 0.646 AC: 6793 AN: 10520

Middle Eastern (MID) AF: 0.619 AC: 182 AN: 294

European-Non Finnish (NFE) AF: 0.615 AC: 41779 AN: 67944

Other (OTH) AF: 0.643 AC: 1352 AN: 2102

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
PhyloP100		0.062

Splicing

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

Other links and lift over

dbSNP: rs4718827; hg19: chr7-68354531;