rs145241704

chr7-141805287-T-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.0755 in 152,158 control chromosomes in the GnomAD database, including 553 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 0.075 (553 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.92

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.44).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.212 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: 0.0755 AC: 11477 AN: 152040 Hom.: 551 Cov.: 31

Gnomad AFR AF: 0.0942

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0492

Gnomad ASJ AF: 0.0507

Gnomad EAS AF: 0.223

Gnomad SAS AF: 0.119

Gnomad FIN AF: 0.0743

Gnomad MID AF: 0.0446

Gnomad NFE AF: 0.0586

Gnomad OTH AF: 0.0617

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

GnomAD4 genome AF: 0.0755 AC: 11485 AN: 152158 Hom.: 553 Cov.: 31 AF XY: 0.0769 AC XY: 5718 AN XY: 74372

Gnomad4 AFR AF: 0.0941

Gnomad4 AMR AF: 0.0491

Gnomad4 ASJ AF: 0.0507

Gnomad4 EAS AF: 0.223

Gnomad4 SAS AF: 0.119

Gnomad4 FIN AF: 0.0743

Gnomad4 NFE AF: 0.0586

Gnomad4 OTH AF: 0.0639

Alfa AF: 0.0710 Hom.: 51

Bravo AF: 0.0746

Asia WGS AF: 0.167 AC: 580 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.44
Cadd	Benign	3.3
Dann	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs145241704; hg19: chr7-141505087;