7-154902677-C-T

Position:

• chr7-154902677-C-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 0.827 in 152,234 control chromosomes in the GnomAD database, including 52,283 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 0.83 (52283 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0380

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.909 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.154902677C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.827 AC: 125837 AN: 152116 Hom.: 52238 Cov.: 32

Gnomad AFR AF: 0.917

Gnomad AMI AF: 0.820

Gnomad AMR AF: 0.831

Gnomad ASJ AF: 0.799

Gnomad EAS AF: 0.741

Gnomad SAS AF: 0.762

Gnomad FIN AF: 0.808

Gnomad MID AF: 0.794

Gnomad NFE AF: 0.788

Gnomad OTH AF: 0.815

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

GnomAD4 genome AF: 0.827 AC: 125943 AN: 152234 Hom.: 52283 Cov.: 32 AF XY: 0.826 AC XY: 61448 AN XY: 74424

Gnomad4 AFR AF: 0.917

Gnomad4 AMR AF: 0.831

Gnomad4 ASJ AF: 0.799

Gnomad4 EAS AF: 0.741

Gnomad4 SAS AF: 0.762

Gnomad4 FIN AF: 0.808

Gnomad4 NFE AF: 0.788

Gnomad4 OTH AF: 0.816

Alfa AF: 0.797 Hom.: 79848

Bravo AF: 0.834

Asia WGS AF: 0.802 AC: 2787 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.7
DANN	Benign	0.18

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2002865; hg19: chr7-154694387;