7-141889478-T-C

Variant names:

• chr7-141889478-T-C
• rs1285957

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;