chr4-72152241-T-G

Variant names:

• chr4-72152241-T-G
• rs17775309

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 0.249 in 152,116 control chromosomes in the GnomAD database, including 5,792 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 0.25 (5792 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0580

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.337 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: 0.249 AC: 37833 AN: 151998 Hom.: 5791 Cov.: 32

Gnomad AFR AF: 0.0896

Gnomad AMI AF: 0.324

Gnomad AMR AF: 0.223

Gnomad ASJ AF: 0.351

Gnomad EAS AF: 0.0223

Gnomad SAS AF: 0.246

Gnomad FIN AF: 0.379

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.341

Gnomad OTH AF: 0.281

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

GnomAD4 genome AF: 0.249 AC: 37825 AN: 152116 Hom.: 5792 Cov.: 32 AF XY: 0.248 AC XY: 18461 AN XY: 74360

Gnomad4 AFR AF: 0.0894

Gnomad4 AMR AF: 0.223

Gnomad4 ASJ AF: 0.351

Gnomad4 EAS AF: 0.0226

Gnomad4 SAS AF: 0.245

Gnomad4 FIN AF: 0.379

Gnomad4 NFE AF: 0.341

Gnomad4 OTH AF: 0.279

Alfa AF: 0.249 Hom.: 1196

Bravo AF: 0.232

Asia WGS AF: 0.136 AC: 474 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	7.0
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17775309; hg19: chr4-73017958;