14-103356425-C-G

Variant names:

• chr14-103356425-C-G
• rs17616316

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 0.0752 in 151,672 control chromosomes in the GnomAD database, including 480 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 0.075 (480 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.646
• Publications: 19 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.106 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: 0.0752 AC: 11396 AN: 151554 Hom.: 477 Cov.: 31

Gnomad AFR AF: 0.109

Gnomad AMI AF: 0.0802

Gnomad AMR AF: 0.0902

Gnomad ASJ AF: 0.0306

Gnomad EAS AF: 0.0478

Gnomad SAS AF: 0.104

Gnomad FIN AF: 0.0703

Gnomad MID AF: 0.0382

Gnomad NFE AF: 0.0548

Gnomad OTH AF: 0.0716

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

GnomAD4 genome AF: 0.0752 AC: 11409 AN: 151672 Hom.: 480 Cov.: 31 AF XY: 0.0770 AC XY: 5709 AN XY: 74132

African (AFR) AF: 0.109 AC: 4498 AN: 41304

American (AMR) AF: 0.0899 AC: 1369 AN: 15222

Ashkenazi Jewish (ASJ) AF: 0.0306 AC: 106 AN: 3468

East Asian (EAS) AF: 0.0478 AC: 247 AN: 5172

South Asian (SAS) AF: 0.103 AC: 490 AN: 4776

European-Finnish (FIN) AF: 0.0703 AC: 741 AN: 10542

Middle Eastern (MID) AF: 0.0411 AC: 12 AN: 292

European-Non Finnish (NFE) AF: 0.0548 AC: 3719 AN: 67884

Other (OTH) AF: 0.0733 AC: 154 AN: 2102

Alfa AF: 0.0598 Hom.: 35

Bravo AF: 0.0786

Asia WGS AF: 0.0810 AC: 282 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.48
DANN	Benign	0.67
PhyloP100		-0.65

Splicing

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

Other links and lift over

dbSNP: rs17616316; hg19: chr14-103822762;