rs4577002

Variant names:

• chr14-84664820-T-C
• rs4577002

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 0.117 in 152,254 control chromosomes in the GnomAD database, including 1,356 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 0.12 (1356 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.299
• Publications: 1 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 (EAS) allele frequency at 95% confidence interval = 0.291 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: 0.117 AC: 17773 AN: 152136 Hom.: 1351 Cov.: 32

Gnomad AFR AF: 0.148

Gnomad AMI AF: 0.0495

Gnomad AMR AF: 0.207

Gnomad ASJ AF: 0.0452

Gnomad EAS AF: 0.303

Gnomad SAS AF: 0.161

Gnomad FIN AF: 0.0627

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0737

Gnomad OTH AF: 0.113

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

GnomAD4 genome AF: 0.117 AC: 17793 AN: 152254 Hom.: 1356 Cov.: 32 AF XY: 0.121 AC XY: 8983 AN XY: 74446

African (AFR) AF: 0.148 AC: 6139 AN: 41538

American (AMR) AF: 0.208 AC: 3173 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0452 AC: 157 AN: 3472

East Asian (EAS) AF: 0.304 AC: 1573 AN: 5178

South Asian (SAS) AF: 0.160 AC: 774 AN: 4830

European-Finnish (FIN) AF: 0.0627 AC: 665 AN: 10612

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.0736 AC: 5009 AN: 68022

Other (OTH) AF: 0.112 AC: 236 AN: 2108

Alfa AF: 0.0918 Hom.: 983

Bravo AF: 0.128

Asia WGS AF: 0.211 AC: 731 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.4
DANN	Benign	0.39
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs4577002; hg19: chr14-85131164;