chr7-86504881-C-A

Variant names:

• chr7-86504881-C-A
• rs3897749

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.0647 AC: 2686 AN: 41534

American (AMR) AF: 0.0962 AC: 1470 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.101 AC: 352 AN: 3468

East Asian (EAS) AF: 0.0674 AC: 349 AN: 5176

South Asian (SAS) AF: 0.0813 AC: 392 AN: 4822

European-Finnish (FIN) AF: 0.0914 AC: 969 AN: 10596

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.105 AC: 7121 AN: 68004

Other (OTH) AF: 0.107 AC: 227 AN: 2116

Alfa AF: 0.107 Hom.: 1513

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
PhyloP100		0.70

Splicing

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

Other links and lift over

dbSNP: rs3897749; hg19: chr7-86134197;