7-16744319-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 0.683 in 152,144 control chromosomes in the GnomAD database, including 37,374 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 0.68 (37374 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00700

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.919 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: 0.683 AC: 103851 AN: 152026 Hom.: 37318 Cov.: 32

Gnomad AFR AF: 0.926

Gnomad AMI AF: 0.730

Gnomad AMR AF: 0.627

Gnomad ASJ AF: 0.607

Gnomad EAS AF: 0.502

Gnomad SAS AF: 0.577

Gnomad FIN AF: 0.510

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.601

Gnomad OTH AF: 0.643

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

GnomAD4 genome AF: 0.683 AC: 103970 AN: 152144 Hom.: 37374 Cov.: 32 AF XY: 0.678 AC XY: 50400 AN XY: 74366

Gnomad4 AFR AF: 0.926

Gnomad4 AMR AF: 0.627

Gnomad4 ASJ AF: 0.607

Gnomad4 EAS AF: 0.501

Gnomad4 SAS AF: 0.576

Gnomad4 FIN AF: 0.510

Gnomad4 NFE AF: 0.601

Gnomad4 OTH AF: 0.644

Alfa AF: 0.634 Hom.: 6488

Bravo AF: 0.699

Asia WGS AF: 0.609 AC: 2115 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	7.6
Dann	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1723804; hg19: chr7-16783944;