rs7197475

Variant names:

• chr16-30631546-C-T
• rs7197475

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 0.462 in 151,856 control chromosomes in the GnomAD database, including 18,778 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 0.46 (18778 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.16

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.722 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: 0.462 AC: 70073 AN: 151738 Hom.: 18756 Cov.: 31

Gnomad AFR AF: 0.729

Gnomad AMI AF: 0.423

Gnomad AMR AF: 0.327

Gnomad ASJ AF: 0.359

Gnomad EAS AF: 0.113

Gnomad SAS AF: 0.698

Gnomad FIN AF: 0.335

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.366

Gnomad OTH AF: 0.415

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

GnomAD4 genome AF: 0.462 AC: 70131 AN: 151856 Hom.: 18778 Cov.: 31 AF XY: 0.460 AC XY: 34164 AN XY: 74196

Gnomad4 AFR AF: 0.729

Gnomad4 AMR AF: 0.327

Gnomad4 ASJ AF: 0.359

Gnomad4 EAS AF: 0.113

Gnomad4 SAS AF: 0.697

Gnomad4 FIN AF: 0.335

Gnomad4 NFE AF: 0.366

Gnomad4 OTH AF: 0.416

Alfa AF: 0.372 Hom.: 18075

Bravo AF: 0.460

Asia WGS AF: 0.464 AC: 1611 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.24
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7197475; hg19: chr16-30642867;