chr7-108141755-A-G

Variant names:

• chr7-108141755-A-G
• rs382140

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 0.748 in 151,680 control chromosomes in the GnomAD database, including 43,257 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 0.75 (43257 hom., cov: 27)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.01
• Publications: 19 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.812 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: 0.748 AC: 113433 AN: 151562 Hom.: 43252 Cov.: 27

Gnomad AFR AF: 0.594

Gnomad AMI AF: 0.845

Gnomad AMR AF: 0.824

Gnomad ASJ AF: 0.872

Gnomad EAS AF: 0.808

Gnomad SAS AF: 0.776

Gnomad FIN AF: 0.736

Gnomad MID AF: 0.807

Gnomad NFE AF: 0.812

Gnomad OTH AF: 0.773

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

GnomAD4 genome AF: 0.748 AC: 113490 AN: 151680 Hom.: 43257 Cov.: 27 AF XY: 0.748 AC XY: 55395 AN XY: 74094

African (AFR) AF: 0.593 AC: 24506 AN: 41296

American (AMR) AF: 0.824 AC: 12564 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.872 AC: 3024 AN: 3468

East Asian (EAS) AF: 0.808 AC: 4127 AN: 5110

South Asian (SAS) AF: 0.777 AC: 3720 AN: 4790

European-Finnish (FIN) AF: 0.736 AC: 7754 AN: 10532

Middle Eastern (MID) AF: 0.796 AC: 234 AN: 294

European-Non Finnish (NFE) AF: 0.812 AC: 55167 AN: 67928

Other (OTH) AF: 0.772 AC: 1628 AN: 2110

Alfa AF: 0.795 Hom.: 192397

Bravo AF: 0.747

Asia WGS AF: 0.769 AC: 2676 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	6.4
DANN	Benign	0.61
PhyloP100		2.0

Splicing

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

Other links and lift over

dbSNP: rs382140; hg19: chr7-107782200;