rs145241704

Variant names:

• chr7-141805287-T-G
• rs145241704

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.0941 AC: 3907 AN: 41502

American (AMR) AF: 0.0491 AC: 751 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0507 AC: 176 AN: 3470

East Asian (EAS) AF: 0.223 AC: 1148 AN: 5156

South Asian (SAS) AF: 0.119 AC: 577 AN: 4830

European-Finnish (FIN) AF: 0.0743 AC: 788 AN: 10600

Middle Eastern (MID) AF: 0.0445 AC: 13 AN: 292

European-Non Finnish (NFE) AF: 0.0586 AC: 3987 AN: 67990

Other (OTH) AF: 0.0639 AC: 135 AN: 2114

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
PhyloP100		3.9

Splicing

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

Other links and lift over

dbSNP: rs145241704; hg19: chr7-141505087;