7-141889478-T-C

Position:

• chr7-141889478-T-C

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 0.858 in 152,128 control chromosomes in the GnomAD database, including 56,095 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 0.86 (56095 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.739

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.91 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: 0.858 AC: 130369 AN: 152010 Hom.: 56048 Cov.: 31

Gnomad AFR AF: 0.918

Gnomad AMI AF: 0.893

Gnomad AMR AF: 0.857

Gnomad ASJ AF: 0.869

Gnomad EAS AF: 0.748

Gnomad SAS AF: 0.830

Gnomad FIN AF: 0.845

Gnomad MID AF: 0.858

Gnomad NFE AF: 0.833

Gnomad OTH AF: 0.840

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

GnomAD4 genome AF: 0.858 AC: 130475 AN: 152128 Hom.: 56095 Cov.: 31 AF XY: 0.856 AC XY: 63670 AN XY: 74350

Gnomad4 AFR AF: 0.918

Gnomad4 AMR AF: 0.858

Gnomad4 ASJ AF: 0.869

Gnomad4 EAS AF: 0.748

Gnomad4 SAS AF: 0.830

Gnomad4 FIN AF: 0.845

Gnomad4 NFE AF: 0.833

Gnomad4 OTH AF: 0.839

Alfa AF: 0.856 Hom.: 6928

Bravo AF: 0.860

Asia WGS AF: 0.794 AC: 2759 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	6.0
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1285957; hg19: chr7-141589278;