rs7678651

Variant names:

• chr4-89847220-C-A
• rs7678651

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 0.306 in 151,952 control chromosomes in the GnomAD database, including 8,048 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 0.31 (8048 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.927

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.39 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: 0.306 AC: 46467 AN: 151834 Hom.: 8053 Cov.: 32

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.379

Gnomad AMR AF: 0.265

Gnomad ASJ AF: 0.324

Gnomad EAS AF: 0.300

Gnomad SAS AF: 0.225

Gnomad FIN AF: 0.428

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.394

Gnomad OTH AF: 0.284

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

GnomAD4 genome AF: 0.306 AC: 46455 AN: 151952 Hom.: 8048 Cov.: 32 AF XY: 0.304 AC XY: 22561 AN XY: 74274

Gnomad4 AFR AF: 0.154

Gnomad4 AMR AF: 0.265

Gnomad4 ASJ AF: 0.324

Gnomad4 EAS AF: 0.300

Gnomad4 SAS AF: 0.225

Gnomad4 FIN AF: 0.428

Gnomad4 NFE AF: 0.394

Gnomad4 OTH AF: 0.280

Alfa AF: 0.363 Hom.: 2875

Bravo AF: 0.287

Asia WGS AF: 0.232 AC: 809 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.59
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7678651; hg19: chr4-90768371;