7-128935498-C-G

Variant names:

• chr7-128935498-C-G
• rs3778754

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 0.401 in 152,144 control chromosomes in the GnomAD database, including 12,915 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 0.40 (12915 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.178

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.457 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: 0.401 AC: 61034 AN: 152026 Hom.: 12915 Cov.: 33

Gnomad AFR AF: 0.301

Gnomad AMI AF: 0.463

Gnomad AMR AF: 0.415

Gnomad ASJ AF: 0.582

Gnomad EAS AF: 0.190

Gnomad SAS AF: 0.433

Gnomad FIN AF: 0.406

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.461

Gnomad OTH AF: 0.451

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

GnomAD4 genome AF: 0.401 AC: 61056 AN: 152144 Hom.: 12915 Cov.: 33 AF XY: 0.396 AC XY: 29457 AN XY: 74372

Gnomad4 AFR AF: 0.301

Gnomad4 AMR AF: 0.414

Gnomad4 ASJ AF: 0.582

Gnomad4 EAS AF: 0.190

Gnomad4 SAS AF: 0.432

Gnomad4 FIN AF: 0.406

Gnomad4 NFE AF: 0.461

Gnomad4 OTH AF: 0.448

Alfa AF: 0.415 Hom.: 1646

Bravo AF: 0.398

Asia WGS AF: 0.291 AC: 1014 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.1
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3778754; hg19: chr7-128575552;