chr14-84958789-T-C

Variant names:

• chr14-84958789-T-C
• rs8007849

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 0.251 in 151,988 control chromosomes in the GnomAD database, including 5,059 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 0.25 (5059 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.49).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.334 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: 0.251 AC: 38148 AN: 151870 Hom.: 5039 Cov.: 32

Gnomad AFR AF: 0.338

Gnomad AMI AF: 0.312

Gnomad AMR AF: 0.229

Gnomad ASJ AF: 0.150

Gnomad EAS AF: 0.253

Gnomad SAS AF: 0.142

Gnomad FIN AF: 0.249

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.217

Gnomad OTH AF: 0.236

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

GnomAD4 genome AF: 0.251 AC: 38212 AN: 151988 Hom.: 5059 Cov.: 32 AF XY: 0.249 AC XY: 18516 AN XY: 74272

African (AFR) AF: 0.339 AC: 14047 AN: 41434

American (AMR) AF: 0.229 AC: 3490 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.150 AC: 520 AN: 3468

East Asian (EAS) AF: 0.253 AC: 1303 AN: 5152

South Asian (SAS) AF: 0.141 AC: 680 AN: 4822

European-Finnish (FIN) AF: 0.249 AC: 2632 AN: 10580

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.217 AC: 14717 AN: 67976

Other (OTH) AF: 0.233 AC: 489 AN: 2102

Alfa AF: 0.237 Hom.: 753

Bravo AF: 0.257

Asia WGS AF: 0.194 AC: 677 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.49
CADD	Benign	7.7
DANN	Benign	0.74
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs8007849; hg19: chr14-85425133;