rs4260611

chr4-68518888-G-Cchr4-68518888-G-T

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 0.309 in 123,060 control chromosomes in the GnomAD database, including 12,203 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 0.31 (12203 hom., cov: 19)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.229

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.407 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: 0.309 AC: 38024 AN: 122998 Hom.: 12187 Cov.: 19

Gnomad AFR AF: 0.231

Gnomad AMI AF: 0.386

Gnomad AMR AF: 0.415

Gnomad ASJ AF: 0.276

Gnomad EAS AF: 0.389

Gnomad SAS AF: 0.295

Gnomad FIN AF: 0.396

Gnomad MID AF: 0.183

Gnomad NFE AF: 0.326

Gnomad OTH AF: 0.277

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

GnomAD4 genome AF: 0.309 AC: 38066 AN: 123060 Hom.: 12203 Cov.: 19 AF XY: 0.313 AC XY: 18341 AN XY: 58564

Gnomad4 AFR AF: 0.232

Gnomad4 AMR AF: 0.416

Gnomad4 ASJ AF: 0.276

Gnomad4 EAS AF: 0.393

Gnomad4 SAS AF: 0.295

Gnomad4 FIN AF: 0.396

Gnomad4 NFE AF: 0.326

Gnomad4 OTH AF: 0.273

Alfa AF: 0.270 Hom.: 982

Asia WGS AF: 0.247 AC: 466 AN: 1886

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	2.3
Dann	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4260611; hg19: chr4-69384606;