chr14-61676555-G-C

Position:

• chr14-61676555-G-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 0.11 in 152,282 control chromosomes in the GnomAD database, including 1,101 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 0.11 (1101 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0360

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.268 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.61676555G>C		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.110 AC: 16793 AN: 152164 Hom.: 1104 Cov.: 33

Gnomad AFR AF: 0.0765

Gnomad AMI AF: 0.130

Gnomad AMR AF: 0.105

Gnomad ASJ AF: 0.239

Gnomad EAS AF: 0.197

Gnomad SAS AF: 0.280

Gnomad FIN AF: 0.0420

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.116

Gnomad OTH AF: 0.129

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

GnomAD4 genome AF: 0.110 AC: 16781 AN: 152282 Hom.: 1101 Cov.: 33 AF XY: 0.112 AC XY: 8315 AN XY: 74460

Gnomad4 AFR AF: 0.0763

Gnomad4 AMR AF: 0.105

Gnomad4 ASJ AF: 0.239

Gnomad4 EAS AF: 0.196

Gnomad4 SAS AF: 0.281

Gnomad4 FIN AF: 0.0420

Gnomad4 NFE AF: 0.116

Gnomad4 OTH AF: 0.128

Alfa AF: 0.0455 Hom.: 38

Bravo AF: 0.112

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.6
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11846496; hg19: chr14-62143273;