rs4899685

Variant names:

• chr14-77954715-G-A
• rs4899685

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 0.217 in 152,168 control chromosomes in the GnomAD database, including 4,100 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 0.22 (4100 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.124
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.292 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: 0.217 AC: 33049 AN: 152050 Hom.: 4103 Cov.: 32

Gnomad AFR AF: 0.0909

Gnomad AMI AF: 0.228

Gnomad AMR AF: 0.300

Gnomad ASJ AF: 0.280

Gnomad EAS AF: 0.281

Gnomad SAS AF: 0.250

Gnomad FIN AF: 0.236

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.261

Gnomad OTH AF: 0.242

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

GnomAD4 genome AF: 0.217 AC: 33060 AN: 152168 Hom.: 4100 Cov.: 32 AF XY: 0.217 AC XY: 16150 AN XY: 74400

African (AFR) AF: 0.0909 AC: 3774 AN: 41534

American (AMR) AF: 0.300 AC: 4579 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.280 AC: 971 AN: 3470

East Asian (EAS) AF: 0.282 AC: 1462 AN: 5182

South Asian (SAS) AF: 0.250 AC: 1204 AN: 4820

European-Finnish (FIN) AF: 0.236 AC: 2501 AN: 10582

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.261 AC: 17759 AN: 67980

Other (OTH) AF: 0.242 AC: 511 AN: 2114

Alfa AF: 0.252 Hom.: 7521

Bravo AF: 0.218

Asia WGS AF: 0.227 AC: 788 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	1.5
DANN	Benign	0.40
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs4899685; hg19: chr14-78421058;