rs3897749

Positions:

• chr7-86504881-C-A

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 0.0902 in 152,194 control chromosomes in the GnomAD database, including 685 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 0.090 (685 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.703

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.103 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: 0.0903 AC: 13730 AN: 152076 Hom.: 685 Cov.: 32

Gnomad AFR AF: 0.0649

Gnomad AMI AF: 0.134

Gnomad AMR AF: 0.0966

Gnomad ASJ AF: 0.101

Gnomad EAS AF: 0.0675

Gnomad SAS AF: 0.0812

Gnomad FIN AF: 0.0914

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.105

Gnomad OTH AF: 0.106

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

GnomAD4 genome AF: 0.0902 AC: 13725 AN: 152194 Hom.: 685 Cov.: 32 AF XY: 0.0900 AC XY: 6697 AN XY: 74404

Gnomad4 AFR AF: 0.0647

Gnomad4 AMR AF: 0.0962

Gnomad4 ASJ AF: 0.101

Gnomad4 EAS AF: 0.0674

Gnomad4 SAS AF: 0.0813

Gnomad4 FIN AF: 0.0914

Gnomad4 NFE AF: 0.105

Gnomad4 OTH AF: 0.107

Alfa AF: 0.108 Hom.: 1184

Bravo AF: 0.0916

Asia WGS AF: 0.0990 AC: 344 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.4
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3897749; hg19: chr7-86134197;