14-60238751-G-C

Variant names:

• chr14-60238751-G-C
• rs6573298

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 0.364 in 152,006 control chromosomes in the GnomAD database, including 11,343 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 0.36 (11343 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0700
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.553 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: 0.364 AC: 55292 AN: 151888 Hom.: 11323 Cov.: 32

Gnomad AFR AF: 0.558

Gnomad AMI AF: 0.0877

Gnomad AMR AF: 0.275

Gnomad ASJ AF: 0.403

Gnomad EAS AF: 0.151

Gnomad SAS AF: 0.453

Gnomad FIN AF: 0.261

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.294

Gnomad OTH AF: 0.341

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

GnomAD4 genome AF: 0.364 AC: 55356 AN: 152006 Hom.: 11343 Cov.: 32 AF XY: 0.359 AC XY: 26641 AN XY: 74306

African (AFR) AF: 0.559 AC: 23159 AN: 41448

American (AMR) AF: 0.274 AC: 4189 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.403 AC: 1400 AN: 3470

East Asian (EAS) AF: 0.151 AC: 782 AN: 5168

South Asian (SAS) AF: 0.450 AC: 2170 AN: 4820

European-Finnish (FIN) AF: 0.261 AC: 2757 AN: 10570

Middle Eastern (MID) AF: 0.395 AC: 116 AN: 294

European-Non Finnish (NFE) AF: 0.294 AC: 19989 AN: 67942

Other (OTH) AF: 0.338 AC: 714 AN: 2110

Alfa AF: 0.156 Hom.: 283

Bravo AF: 0.370

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.30
DANN	Benign	0.38
PhyloP100		0.070

Splicing

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

Other links and lift over

dbSNP: rs6573298; hg19: chr14-60705469;