rs7427984

Variant names:

• chr3-68959094-G-A
• rs7427984

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 0.479 in 151,930 control chromosomes in the GnomAD database, including 18,517 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 0.48 (18517 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.49

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.564 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: 0.480 AC: 72806 AN: 151812 Hom.: 18511 Cov.: 31

Gnomad AFR AF: 0.425

Gnomad AMI AF: 0.492

Gnomad AMR AF: 0.423

Gnomad ASJ AF: 0.613

Gnomad EAS AF: 0.0847

Gnomad SAS AF: 0.323

Gnomad FIN AF: 0.409

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.569

Gnomad OTH AF: 0.524

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

GnomAD4 genome AF: 0.479 AC: 72832 AN: 151930 Hom.: 18517 Cov.: 31 AF XY: 0.465 AC XY: 34523 AN XY: 74260

Gnomad4 AFR AF: 0.425

Gnomad4 AMR AF: 0.422

Gnomad4 ASJ AF: 0.613

Gnomad4 EAS AF: 0.0845

Gnomad4 SAS AF: 0.321

Gnomad4 FIN AF: 0.409

Gnomad4 NFE AF: 0.569

Gnomad4 OTH AF: 0.528

Alfa AF: 0.530 Hom.: 14512

Bravo AF: 0.478

Asia WGS AF: 0.282 AC: 981 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.011
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7427984; hg19: chr3-69008245;