rs7145505

Variant names:

• chr14-60238857-C-G
• rs7145505

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 0.342 in 152,092 control chromosomes in the GnomAD database, including 9,619 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 0.34 (9619 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28
• Publications: 4 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 = 0.482 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: 0.341 AC: 51893 AN: 151974 Hom.: 9601 Cov.: 32

Gnomad AFR AF: 0.487

Gnomad AMI AF: 0.0877

Gnomad AMR AF: 0.266

Gnomad ASJ AF: 0.401

Gnomad EAS AF: 0.128

Gnomad SAS AF: 0.433

Gnomad FIN AF: 0.261

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.293

Gnomad OTH AF: 0.322

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

GnomAD4 genome AF: 0.342 AC: 51951 AN: 152092 Hom.: 9619 Cov.: 32 AF XY: 0.337 AC XY: 25034 AN XY: 74358

African (AFR) AF: 0.487 AC: 20222 AN: 41482

American (AMR) AF: 0.266 AC: 4062 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.401 AC: 1393 AN: 3470

East Asian (EAS) AF: 0.129 AC: 665 AN: 5174

South Asian (SAS) AF: 0.430 AC: 2078 AN: 4828

European-Finnish (FIN) AF: 0.261 AC: 2759 AN: 10582

Middle Eastern (MID) AF: 0.384 AC: 113 AN: 294

European-Non Finnish (NFE) AF: 0.293 AC: 19907 AN: 67956

Other (OTH) AF: 0.318 AC: 672 AN: 2110

Alfa AF: 0.314 Hom.: 1023

Bravo AF: 0.346

Asia WGS AF: 0.271 AC: 944 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.23
DANN	Benign	0.61
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs7145505; hg19: chr14-60705575;