rs6840987

Variant names:

• chr4-137346966-C-A
• rs6840987

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 0.398 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
• 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 (EAS) allele frequency at 95% confidence interval = 0.471 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: 0.398 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

African (AFR) AF: 0.327 AC: 13539 AN: 41426

American (AMR) AF: 0.434 AC: 6623 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.333 AC: 1156 AN: 3468

East Asian (EAS) AF: 0.487 AC: 2509 AN: 5148

South Asian (SAS) AF: 0.307 AC: 1480 AN: 4824

European-Finnish (FIN) AF: 0.499 AC: 5253 AN: 10522

Middle Eastern (MID) AF: 0.414 AC: 121 AN: 292

European-Non Finnish (NFE) AF: 0.419 AC: 28448 AN: 67948

Other (OTH) AF: 0.367 AC: 773 AN: 2104

Alfa AF: 0.400 Hom.: 1591

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
PhyloP100		-2.5

Splicing

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

Other links and lift over

dbSNP: rs6840987; hg19: chr4-138268120;