rs7204252

Variant names:

• chr16-29852848-C-T
• rs7204252

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 0.989 in 152,314 control chromosomes in the GnomAD database, including 74,537 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 0.99 (74537 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.69

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.993 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: 0.989 AC: 150511 AN: 152196 Hom.: 74486 Cov.: 32

Gnomad AFR AF: 0.993

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.957

Gnomad ASJ AF: 1.00

Gnomad EAS AF: 0.899

Gnomad SAS AF: 0.977

Gnomad FIN AF: 0.998

Gnomad MID AF: 1.00

Gnomad NFE AF: 0.999

Gnomad OTH AF: 0.990

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

GnomAD4 genome AF: 0.989 AC: 150621 AN: 152314 Hom.: 74537 Cov.: 32 AF XY: 0.988 AC XY: 73572 AN XY: 74476

Gnomad4 AFR AF: 0.993

Gnomad4 AMR AF: 0.957

Gnomad4 ASJ AF: 1.00

Gnomad4 EAS AF: 0.898

Gnomad4 SAS AF: 0.977

Gnomad4 FIN AF: 0.998

Gnomad4 NFE AF: 0.999

Gnomad4 OTH AF: 0.989

Alfa AF: 0.994 Hom.: 10421

Bravo AF: 0.985

Asia WGS AF: 0.942 AC: 3278 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.22
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7204252; hg19: chr16-29864169;