7-87499549-T-C

Position:

• chr7-87499549-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 0.18 in 151,970 control chromosomes in the GnomAD database, including 3,117 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 0.18 (3117 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.107

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.245 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.180 AC: 27331 AN: 151852 Hom.: 3113 Cov.: 31

Gnomad AFR AF: 0.0498

Gnomad AMI AF: 0.179

Gnomad AMR AF: 0.252

Gnomad ASJ AF: 0.344

Gnomad EAS AF: 0.130

Gnomad SAS AF: 0.196

Gnomad FIN AF: 0.147

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.241

Gnomad OTH AF: 0.231

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

GnomAD4 genome AF: 0.180 AC: 27333 AN: 151970 Hom.: 3117 Cov.: 31 AF XY: 0.179 AC XY: 13262 AN XY: 74262

Gnomad4 AFR AF: 0.0496

Gnomad4 AMR AF: 0.252

Gnomad4 ASJ AF: 0.344

Gnomad4 EAS AF: 0.131

Gnomad4 SAS AF: 0.198

Gnomad4 FIN AF: 0.147

Gnomad4 NFE AF: 0.241

Gnomad4 OTH AF: 0.227

Alfa AF: 0.235 Hom.: 6702

Bravo AF: 0.180

Asia WGS AF: 0.160 AC: 556 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.9
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6946119; hg19: chr7-87128865;