7-16744319-T-C

Variant names:

• chr7-16744319-T-C
• rs1723804

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;