chr6-98542613-T-C

Variant names:

• chr6-98542613-T-C
• rs6904416

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;