rs6901498

Variant names:

• chr6-71735860-G-C
• rs6901498

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 0.349 in 151,854 control chromosomes in the GnomAD database, including 9,497 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 0.35 (9497 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.59

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.38 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: 0.350 AC: 53041 AN: 151736 Hom.: 9498 Cov.: 32

Gnomad AFR AF: 0.278

Gnomad AMI AF: 0.365

Gnomad AMR AF: 0.315

Gnomad ASJ AF: 0.413

Gnomad EAS AF: 0.337

Gnomad SAS AF: 0.323

Gnomad FIN AF: 0.455

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.384

Gnomad OTH AF: 0.350

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

GnomAD4 genome AF: 0.349 AC: 53053 AN: 151854 Hom.: 9497 Cov.: 32 AF XY: 0.350 AC XY: 25991 AN XY: 74196

Gnomad4 AFR AF: 0.277

Gnomad4 AMR AF: 0.316

Gnomad4 ASJ AF: 0.413

Gnomad4 EAS AF: 0.337

Gnomad4 SAS AF: 0.324

Gnomad4 FIN AF: 0.455

Gnomad4 NFE AF: 0.384

Gnomad4 OTH AF: 0.346

Alfa AF: 0.379 Hom.: 1358

Bravo AF: 0.333

Asia WGS AF: 0.272 AC: 946 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.0
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6901498; hg19: chr6-72445563;