rs4307025

chr4-110736347-T-Achr4-110736347-T-C

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 0.375 in 151,954 control chromosomes in the GnomAD database, including 11,651 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 0.38 (11651 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.202

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.711 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.375 AC: 56979 AN: 151836 Hom.: 11622 Cov.: 31

Gnomad AFR AF: 0.449

Gnomad AMI AF: 0.297

Gnomad AMR AF: 0.474

Gnomad ASJ AF: 0.477

Gnomad EAS AF: 0.729

Gnomad SAS AF: 0.393

Gnomad FIN AF: 0.355

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.279

Gnomad OTH AF: 0.369

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

GnomAD4 genome AF: 0.375 AC: 57051 AN: 151954 Hom.: 11651 Cov.: 31 AF XY: 0.389 AC XY: 28883 AN XY: 74278

Gnomad4 AFR AF: 0.449

Gnomad4 AMR AF: 0.474

Gnomad4 ASJ AF: 0.477

Gnomad4 EAS AF: 0.730

Gnomad4 SAS AF: 0.393

Gnomad4 FIN AF: 0.355

Gnomad4 NFE AF: 0.280

Gnomad4 OTH AF: 0.370

Alfa AF: 0.182 Hom.: 344

Bravo AF: 0.389

Asia WGS AF: 0.542 AC: 1876 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	1.7
Dann	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4307025; hg19: chr4-111657503;