chr14-35390868-C-T

Variant names:

• chr14-35390868-C-T
• rs743228

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 0.498 in 152,082 control chromosomes in the GnomAD database, including 19,193 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 (19193 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.251
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.575 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.498 AC: 75694 AN: 151964 Hom.: 19159 Cov.: 33

Gnomad AFR AF: 0.558

Gnomad AMI AF: 0.501

Gnomad AMR AF: 0.585

Gnomad ASJ AF: 0.503

Gnomad EAS AF: 0.410

Gnomad SAS AF: 0.520

Gnomad FIN AF: 0.386

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.464

Gnomad OTH AF: 0.512

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

GnomAD4 genome AF: 0.498 AC: 75780 AN: 152082 Hom.: 19193 Cov.: 33 AF XY: 0.496 AC XY: 36857 AN XY: 74358

African (AFR) AF: 0.559 AC: 23175 AN: 41476

American (AMR) AF: 0.586 AC: 8949 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.503 AC: 1747 AN: 3470

East Asian (EAS) AF: 0.411 AC: 2122 AN: 5158

South Asian (SAS) AF: 0.521 AC: 2509 AN: 4820

European-Finnish (FIN) AF: 0.386 AC: 4090 AN: 10598

Middle Eastern (MID) AF: 0.524 AC: 154 AN: 294

European-Non Finnish (NFE) AF: 0.463 AC: 31497 AN: 67956

Other (OTH) AF: 0.510 AC: 1080 AN: 2116

Alfa AF: 0.480 Hom.: 11523

Bravo AF: 0.516

Asia WGS AF: 0.473 AC: 1650 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.0
DANN	Benign	0.70
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs743228; hg19: chr14-35860074;