rs7214466

chr17-40461852-T-Cchr17-40461852-T-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 0.384 in 151,952 control chromosomes in the GnomAD database, including 11,830 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 0.38 (11830 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.47

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.523 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: 0.384 AC: 58368 AN: 151832 Hom.: 11821 Cov.: 32

Gnomad AFR AF: 0.529

Gnomad AMI AF: 0.248

Gnomad AMR AF: 0.408

Gnomad ASJ AF: 0.380

Gnomad EAS AF: 0.407

Gnomad SAS AF: 0.354

Gnomad FIN AF: 0.348

Gnomad MID AF: 0.309

Gnomad NFE AF: 0.301

Gnomad OTH AF: 0.345

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

GnomAD4 genome AF: 0.384 AC: 58415 AN: 151952 Hom.: 11830 Cov.: 32 AF XY: 0.390 AC XY: 28956 AN XY: 74292

Gnomad4 AFR AF: 0.529

Gnomad4 AMR AF: 0.408

Gnomad4 ASJ AF: 0.380

Gnomad4 EAS AF: 0.407

Gnomad4 SAS AF: 0.353

Gnomad4 FIN AF: 0.348

Gnomad4 NFE AF: 0.301

Gnomad4 OTH AF: 0.342

Alfa AF: 0.294 Hom.: 3165

Bravo AF: 0.396

Asia WGS AF: 0.356 AC: 1237 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	7.4
Dann	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7214466; hg19: chr17-38618104;