17-71963822-T-C

Variant names:

• chr17-71963822-T-C
• rs7214582

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 0.947 in 152,268 control chromosomes in the GnomAD database, including 68,420 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 0.95 (68420 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.667

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.981 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: 0.947 AC: 144134 AN: 152150 Hom.: 68364 Cov.: 32

Gnomad AFR AF: 0.989

Gnomad AMI AF: 0.997

Gnomad AMR AF: 0.953

Gnomad ASJ AF: 0.949

Gnomad EAS AF: 0.938

Gnomad SAS AF: 0.924

Gnomad FIN AF: 0.854

Gnomad MID AF: 0.946

Gnomad NFE AF: 0.937

Gnomad OTH AF: 0.943

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

GnomAD4 genome AF: 0.947 AC: 144248 AN: 152268 Hom.: 68420 Cov.: 32 AF XY: 0.943 AC XY: 70217 AN XY: 74434

Gnomad4 AFR AF: 0.989

Gnomad4 AMR AF: 0.953

Gnomad4 ASJ AF: 0.949

Gnomad4 EAS AF: 0.938

Gnomad4 SAS AF: 0.923

Gnomad4 FIN AF: 0.854

Gnomad4 NFE AF: 0.937

Gnomad4 OTH AF: 0.943

Alfa AF: 0.939 Hom.: 83722

Bravo AF: 0.958

Asia WGS AF: 0.941 AC: 3273 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	13
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7214582; hg19: chr17-69959963;