rs7674482

Positions:

• chr4-45865444-T-C
• chr4-45865444-T-G

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.294

Gnomad4 AMR AF: 0.222

Gnomad4 ASJ AF: 0.201

Gnomad4 EAS AF: 0.284

Gnomad4 SAS AF: 0.255

Gnomad4 FIN AF: 0.345

Gnomad4 NFE AF: 0.231

Gnomad4 OTH AF: 0.236

Alfa AF: 0.235 Hom.: 4287

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7674482; hg19: chr4-45867461;