chr14-85753423-T-C

Variant names:

• chr14-85753423-T-C
• rs1957789

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 0.973 in 152,202 control chromosomes in the GnomAD database, including 72,079 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 0.97 (72079 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01
• Publications: 0 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 (AMR) allele frequency at 95% confidence interval = 0.976 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: 0.973 AC: 147969 AN: 152084 Hom.: 72028 Cov.: 31

Gnomad AFR AF: 0.958

Gnomad AMI AF: 0.922

Gnomad AMR AF: 0.986

Gnomad ASJ AF: 0.989

Gnomad EAS AF: 0.971

Gnomad SAS AF: 0.885

Gnomad FIN AF: 0.991

Gnomad MID AF: 0.934

Gnomad NFE AF: 0.982

Gnomad OTH AF: 0.973

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

GnomAD4 genome AF: 0.973 AC: 148079 AN: 152202 Hom.: 72079 Cov.: 31 AF XY: 0.972 AC XY: 72281 AN XY: 74394

African (AFR) AF: 0.958 AC: 39804 AN: 41532

American (AMR) AF: 0.986 AC: 15048 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.989 AC: 3435 AN: 3472

East Asian (EAS) AF: 0.971 AC: 5018 AN: 5170

South Asian (SAS) AF: 0.885 AC: 4268 AN: 4824

European-Finnish (FIN) AF: 0.991 AC: 10532 AN: 10624

Middle Eastern (MID) AF: 0.929 AC: 273 AN: 294

European-Non Finnish (NFE) AF: 0.982 AC: 66807 AN: 67998

Other (OTH) AF: 0.973 AC: 2053 AN: 2110

Alfa AF: 0.975 Hom.: 10618

Bravo AF: 0.974

Asia WGS AF: 0.919 AC: 3196 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	0.29
DANN	Benign	0.86
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs1957789; hg19: chr14-86219767;