rs382140

Positions:

• chr7-108141755-A-G
• chr7-108141755-A-T

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 0.748 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.593

Gnomad4 AMR AF: 0.824

Gnomad4 ASJ AF: 0.872

Gnomad4 EAS AF: 0.808

Gnomad4 SAS AF: 0.777

Gnomad4 FIN AF: 0.736

Gnomad4 NFE AF: 0.812

Gnomad4 OTH AF: 0.772

Alfa AF: 0.807 Hom.: 97607

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs382140; hg19: chr7-107782200;