chr14-97057408-C-T

Variant names:

• chr14-97057408-C-T
• rs724210

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 0.772 in 152,146 control chromosomes in the GnomAD database, including 46,593 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 0.77 (46593 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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.964 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: 0.772 AC: 117394 AN: 152028 Hom.: 46529 Cov.: 32

Gnomad AFR AF: 0.938

Gnomad AMI AF: 0.601

Gnomad AMR AF: 0.799

Gnomad ASJ AF: 0.681

Gnomad EAS AF: 0.986

Gnomad SAS AF: 0.840

Gnomad FIN AF: 0.695

Gnomad MID AF: 0.706

Gnomad NFE AF: 0.664

Gnomad OTH AF: 0.745

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

GnomAD4 genome AF: 0.772 AC: 117519 AN: 152146 Hom.: 46593 Cov.: 32 AF XY: 0.776 AC XY: 57681 AN XY: 74368

African (AFR) AF: 0.938 AC: 38969 AN: 41540

American (AMR) AF: 0.799 AC: 12226 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.681 AC: 2361 AN: 3468

East Asian (EAS) AF: 0.987 AC: 5102 AN: 5170

South Asian (SAS) AF: 0.838 AC: 4041 AN: 4820

European-Finnish (FIN) AF: 0.695 AC: 7345 AN: 10564

Middle Eastern (MID) AF: 0.711 AC: 209 AN: 294

European-Non Finnish (NFE) AF: 0.664 AC: 45147 AN: 67976

Other (OTH) AF: 0.745 AC: 1572 AN: 2110

Alfa AF: 0.703 Hom.: 30051

Bravo AF: 0.787

Asia WGS AF: 0.893 AC: 3105 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.0
DANN	Benign	0.48
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs724210; hg19: chr14-97523745;