rs2047179

chr6-98430936-A-G

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 0.301 in 151,942 control chromosomes in the GnomAD database, including 6,908 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 0.30 (6908 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0200

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.321 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.301 AC: 45625 AN: 151822 Hom.: 6904 Cov.: 32

Gnomad AFR AF: 0.265

Gnomad AMI AF: 0.202

Gnomad AMR AF: 0.282

Gnomad ASJ AF: 0.374

Gnomad EAS AF: 0.258

Gnomad SAS AF: 0.243

Gnomad FIN AF: 0.340

Gnomad MID AF: 0.379

Gnomad NFE AF: 0.325

Gnomad OTH AF: 0.305

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

GnomAD4 genome AF: 0.301 AC: 45663 AN: 151942 Hom.: 6908 Cov.: 32 AF XY: 0.303 AC XY: 22470 AN XY: 74246

Gnomad4 AFR AF: 0.265

Gnomad4 AMR AF: 0.282

Gnomad4 ASJ AF: 0.374

Gnomad4 EAS AF: 0.257

Gnomad4 SAS AF: 0.244

Gnomad4 FIN AF: 0.340

Gnomad4 NFE AF: 0.325

Gnomad4 OTH AF: 0.302

Alfa AF: 0.315 Hom.: 1267

Bravo AF: 0.294

Asia WGS AF: 0.213 AC: 743 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	1.6
Dann	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2047179; hg19: chr6-98878812; COSMIC: COSV69415044;