rs7160413

Positions:

• chr14-100649196-G-A
• chr14-100649196-G-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 0.0848 in 152,194 control chromosomes in the GnomAD database, including 607 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 0.085 (607 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.35

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.139 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: 0.0848 AC: 12892 AN: 152076 Hom.: 606 Cov.: 33

Gnomad AFR AF: 0.100

Gnomad AMI AF: 0.0462

Gnomad AMR AF: 0.0519

Gnomad ASJ AF: 0.133

Gnomad EAS AF: 0.00116

Gnomad SAS AF: 0.148

Gnomad FIN AF: 0.106

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0793

Gnomad OTH AF: 0.0822

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

GnomAD4 genome AF: 0.0848 AC: 12902 AN: 152194 Hom.: 607 Cov.: 33 AF XY: 0.0872 AC XY: 6488 AN XY: 74424

Gnomad4 AFR AF: 0.100

Gnomad4 AMR AF: 0.0518

Gnomad4 ASJ AF: 0.133

Gnomad4 EAS AF: 0.00116

Gnomad4 SAS AF: 0.148

Gnomad4 FIN AF: 0.106

Gnomad4 NFE AF: 0.0793

Gnomad4 OTH AF: 0.0814

Alfa AF: 0.0859 Hom.: 315

Bravo AF: 0.0781

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.0
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7160413; hg19: chr14-101115533;