14-54903622-C-T

Variant names:

• chr14-54903622-C-T
• rs10137071

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 0.415 in 152,054 control chromosomes in the GnomAD database, including 14,823 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 0.41 (14823 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.285
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.638 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: 0.414 AC: 62917 AN: 151936 Hom.: 14784 Cov.: 32

Gnomad AFR AF: 0.644

Gnomad AMI AF: 0.501

Gnomad AMR AF: 0.350

Gnomad ASJ AF: 0.262

Gnomad EAS AF: 0.179

Gnomad SAS AF: 0.369

Gnomad FIN AF: 0.400

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.321

Gnomad OTH AF: 0.368

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

GnomAD4 genome AF: 0.415 AC: 63029 AN: 152054 Hom.: 14823 Cov.: 32 AF XY: 0.415 AC XY: 30832 AN XY: 74310

African (AFR) AF: 0.645 AC: 26727 AN: 41458

American (AMR) AF: 0.349 AC: 5340 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.262 AC: 909 AN: 3470

East Asian (EAS) AF: 0.180 AC: 929 AN: 5162

South Asian (SAS) AF: 0.370 AC: 1781 AN: 4818

European-Finnish (FIN) AF: 0.400 AC: 4228 AN: 10570

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.321 AC: 21818 AN: 67974

Other (OTH) AF: 0.370 AC: 783 AN: 2114

Alfa AF: 0.228 Hom.: 589

Bravo AF: 0.419

Asia WGS AF: 0.332 AC: 1154 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	5.9
DANN	Benign	0.72
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs10137071; hg19: chr14-55370340;