rs2047179

Variant names:

• chr6-98430936-A-G
• rs2047179

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;