chr7-155104083-T-G

Variant names:

• chr7-155104083-T-G
• rs1730143

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.641 in 152,016 control chromosomes in the GnomAD database, including 31,331 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 0.64 (31331 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.27
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.667 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: 0.641 AC: 97311 AN: 151896 Hom.: 31307 Cov.: 33

Gnomad AFR AF: 0.593

Gnomad AMI AF: 0.565

Gnomad AMR AF: 0.652

Gnomad ASJ AF: 0.672

Gnomad EAS AF: 0.616

Gnomad SAS AF: 0.657

Gnomad FIN AF: 0.606

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.673

Gnomad OTH AF: 0.636

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

GnomAD4 genome AF: 0.641 AC: 97379 AN: 152016 Hom.: 31331 Cov.: 33 AF XY: 0.639 AC XY: 47431 AN XY: 74272

African (AFR) AF: 0.593 AC: 24601 AN: 41466

American (AMR) AF: 0.652 AC: 9971 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.672 AC: 2334 AN: 3472

East Asian (EAS) AF: 0.617 AC: 3147 AN: 5098

South Asian (SAS) AF: 0.658 AC: 3167 AN: 4816

European-Finnish (FIN) AF: 0.606 AC: 6398 AN: 10562

Middle Eastern (MID) AF: 0.616 AC: 181 AN: 294

European-Non Finnish (NFE) AF: 0.673 AC: 45733 AN: 67992

Other (OTH) AF: 0.629 AC: 1332 AN: 2116

Alfa AF: 0.550 Hom.: 1709

Bravo AF: 0.640

Asia WGS AF: 0.594 AC: 2068 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.3
DANN	Benign	0.78
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs1730143; hg19: chr7-154895793;