14-100653897-T-G

Variant names:

• chr14-100653897-T-G
• rs1018534

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 0.501 in 152,160 control chromosomes in the GnomAD database, including 22,187 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 0.50 (22187 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -7.85
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.676 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: 0.501 AC: 76173 AN: 152042 Hom.: 22188 Cov.: 33

Gnomad AFR AF: 0.263

Gnomad AMI AF: 0.732

Gnomad AMR AF: 0.441

Gnomad ASJ AF: 0.653

Gnomad EAS AF: 0.0518

Gnomad SAS AF: 0.337

Gnomad FIN AF: 0.577

Gnomad MID AF: 0.674

Gnomad NFE AF: 0.681

Gnomad OTH AF: 0.536

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

GnomAD4 genome AF: 0.501 AC: 76172 AN: 152160 Hom.: 22187 Cov.: 33 AF XY: 0.491 AC XY: 36486 AN XY: 74378

African (AFR) AF: 0.262 AC: 10875 AN: 41502

American (AMR) AF: 0.441 AC: 6743 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.653 AC: 2262 AN: 3466

East Asian (EAS) AF: 0.0519 AC: 269 AN: 5186

South Asian (SAS) AF: 0.339 AC: 1637 AN: 4824

European-Finnish (FIN) AF: 0.577 AC: 6112 AN: 10586

Middle Eastern (MID) AF: 0.673 AC: 198 AN: 294

European-Non Finnish (NFE) AF: 0.681 AC: 46293 AN: 67988

Other (OTH) AF: 0.530 AC: 1120 AN: 2112

Alfa AF: 0.612 Hom.: 79198

Bravo AF: 0.482

Asia WGS AF: 0.182 AC: 632 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.0050
DANN	Benign	0.27
PhyloP100		-7.9

Splicing

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

Other links and lift over

dbSNP: rs1018534; hg19: chr14-101120234;