chr4-45865444-T-C

Variant names:

• chr4-45865444-T-C
• rs7674482

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 0.257 in 151,804 control chromosomes in the GnomAD database, including 5,218 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 0.26 (5218 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0100
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.289 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: 0.257 AC: 38970 AN: 151686 Hom.: 5213 Cov.: 32

Gnomad AFR AF: 0.294

Gnomad AMI AF: 0.216

Gnomad AMR AF: 0.221

Gnomad ASJ AF: 0.201

Gnomad EAS AF: 0.283

Gnomad SAS AF: 0.255

Gnomad FIN AF: 0.345

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.231

Gnomad OTH AF: 0.239

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

GnomAD4 genome AF: 0.257 AC: 38996 AN: 151804 Hom.: 5218 Cov.: 32 AF XY: 0.261 AC XY: 19372 AN XY: 74180

African (AFR) AF: 0.294 AC: 12176 AN: 41450

American (AMR) AF: 0.222 AC: 3383 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.201 AC: 696 AN: 3466

East Asian (EAS) AF: 0.284 AC: 1466 AN: 5160

South Asian (SAS) AF: 0.255 AC: 1231 AN: 4822

European-Finnish (FIN) AF: 0.345 AC: 3640 AN: 10546

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.231 AC: 15661 AN: 67792

Other (OTH) AF: 0.236 AC: 497 AN: 2108

Alfa AF: 0.242 Hom.: 11886

Bravo AF: 0.252

Asia WGS AF: 0.275 AC: 952 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.2
DANN	Benign	0.69
PhyloP100		0.010

Splicing

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

Other links and lift over

dbSNP: rs7674482; hg19: chr4-45867461;