rs6904416

chr6-98542613-T-C

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 0.122 in 152,232 control chromosomes in the GnomAD database, including 1,497 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 0.12 (1497 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.375

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.172 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: 0.122 AC: 18568 AN: 152114 Hom.: 1499 Cov.: 32

Gnomad AFR AF: 0.0325

Gnomad AMI AF: 0.196

Gnomad AMR AF: 0.106

Gnomad ASJ AF: 0.193

Gnomad EAS AF: 0.0297

Gnomad SAS AF: 0.131

Gnomad FIN AF: 0.162

Gnomad MID AF: 0.311

Gnomad NFE AF: 0.175

Gnomad OTH AF: 0.137

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

GnomAD4 genome AF: 0.122 AC: 18561 AN: 152232 Hom.: 1497 Cov.: 32 AF XY: 0.120 AC XY: 8914 AN XY: 74430

Gnomad4 AFR AF: 0.0324

Gnomad4 AMR AF: 0.106

Gnomad4 ASJ AF: 0.193

Gnomad4 EAS AF: 0.0299

Gnomad4 SAS AF: 0.132

Gnomad4 FIN AF: 0.162

Gnomad4 NFE AF: 0.175

Gnomad4 OTH AF: 0.135

Alfa AF: 0.162 Hom.: 1908

Bravo AF: 0.113

Asia WGS AF: 0.0590 AC: 207 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
Cadd	Benign	6.3
Dann	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6904416; hg19: chr6-98990489;