rs16896742

chr6-29954963-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 0.353 in 151,410 control chromosomes in the GnomAD database, including 7,052 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 (7052 hom., cov: 35)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.139

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.364 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: 0.353 AC: 53356 AN: 151292 Hom.: 7051 Cov.: 35

Gnomad AFR AF: 0.322

Gnomad AMI AF: 0.365

Gnomad AMR AF: 0.372

Gnomad ASJ AF: 0.288

Gnomad EAS AF: 0.367

Gnomad SAS AF: 0.317

Gnomad FIN AF: 0.423

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.361

Gnomad OTH AF: 0.336

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

GnomAD4 genome AF: 0.353 AC: 53387 AN: 151410 Hom.: 7052 Cov.: 35 AF XY: 0.353 AC XY: 26126 AN XY: 74026

Gnomad4 AFR AF: 0.322

Gnomad4 AMR AF: 0.372

Gnomad4 ASJ AF: 0.288

Gnomad4 EAS AF: 0.367

Gnomad4 SAS AF: 0.317

Gnomad4 FIN AF: 0.423

Gnomad4 NFE AF: 0.361

Gnomad4 OTH AF: 0.332

Alfa AF: 0.370 Hom.: 3646

Asia WGS AF: 0.306 AC: 1064 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	4.8
Dann	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16896742; hg19: chr6-29922740;