rs1972373

Positions:

• chr14-19977211-T-C
• chr14-19977211-T-G

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 0.381 in 152,026 control chromosomes in the GnomAD database, including 14,012 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 0.38 (14012 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0400

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.69 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.381 AC: 57828 AN: 151906 Hom.: 13977 Cov.: 32

Gnomad AFR AF: 0.696

Gnomad AMI AF: 0.180

Gnomad AMR AF: 0.252

Gnomad ASJ AF: 0.188

Gnomad EAS AF: 0.150

Gnomad SAS AF: 0.347

Gnomad FIN AF: 0.224

Gnomad MID AF: 0.277

Gnomad NFE AF: 0.276

Gnomad OTH AF: 0.340

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

GnomAD4 genome AF: 0.381 AC: 57908 AN: 152026 Hom.: 14012 Cov.: 32 AF XY: 0.375 AC XY: 27875 AN XY: 74308

Gnomad4 AFR AF: 0.697

Gnomad4 AMR AF: 0.252

Gnomad4 ASJ AF: 0.188

Gnomad4 EAS AF: 0.150

Gnomad4 SAS AF: 0.345

Gnomad4 FIN AF: 0.224

Gnomad4 NFE AF: 0.276

Gnomad4 OTH AF: 0.338

Alfa AF: 0.285 Hom.: 8826

Bravo AF: 0.391

Asia WGS AF: 0.275 AC: 955 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	6.0
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1972373; hg19: chr14-20445370;