7-16019555-G-A

Position:

• chr7-16019555-G-A

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4 BA1

The variant allele was found at a frequency of 0.338 in 151,858 control chromosomes in the GnomAD database, including 10,361 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 0.34 (10361 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.52

ACMG classification

Verdict is Benign. Variant got -9 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.15).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.517 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: 0.338 AC: 51293 AN: 151740 Hom.: 10351 Cov.: 31

Gnomad AFR AF: 0.120

Gnomad AMI AF: 0.325

Gnomad AMR AF: 0.438

Gnomad ASJ AF: 0.248

Gnomad EAS AF: 0.464

Gnomad SAS AF: 0.534

Gnomad FIN AF: 0.511

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.404

Gnomad OTH AF: 0.329

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

GnomAD4 genome AF: 0.338 AC: 51321 AN: 151858 Hom.: 10361 Cov.: 31 AF XY: 0.347 AC XY: 25748 AN XY: 74176

Gnomad4 AFR AF: 0.119

Gnomad4 AMR AF: 0.439

Gnomad4 ASJ AF: 0.248

Gnomad4 EAS AF: 0.464

Gnomad4 SAS AF: 0.534

Gnomad4 FIN AF: 0.511

Gnomad4 NFE AF: 0.404

Gnomad4 OTH AF: 0.331

Alfa AF: 0.368 Hom.: 9287

Bravo AF: 0.320

Asia WGS AF: 0.476 AC: 1656 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.15
CADD	Benign	23
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2030972; hg19: chr7-16059180;