rs6840987

Positions:

• chr4-137346966-C-A

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 0.398 in 151,896 control chromosomes in the GnomAD database, including 12,234 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 (12234 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.48

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 (EAS) allele frequency at 95% confidence interval = 0.471 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: 0.398 AC: 60420 AN: 151776 Hom.: 12229 Cov.: 32

Gnomad AFR AF: 0.327

Gnomad AMI AF: 0.588

Gnomad AMR AF: 0.435

Gnomad ASJ AF: 0.333

Gnomad EAS AF: 0.488

Gnomad SAS AF: 0.307

Gnomad FIN AF: 0.499

Gnomad MID AF: 0.417

Gnomad NFE AF: 0.419

Gnomad OTH AF: 0.370

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

GnomAD4 genome AF: 0.398 AC: 60438 AN: 151896 Hom.: 12234 Cov.: 32 AF XY: 0.400 AC XY: 29678 AN XY: 74200

Gnomad4 AFR AF: 0.327

Gnomad4 AMR AF: 0.434

Gnomad4 ASJ AF: 0.333

Gnomad4 EAS AF: 0.487

Gnomad4 SAS AF: 0.307

Gnomad4 FIN AF: 0.499

Gnomad4 NFE AF: 0.419

Gnomad4 OTH AF: 0.367

Alfa AF: 0.403 Hom.: 1550

Bravo AF: 0.393

Asia WGS AF: 0.378 AC: 1311 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.030
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6840987; hg19: chr4-138268120;