rs1972373

Variant names:

• chr14-19977211-T-C
• rs1972373

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.697 AC: 28899 AN: 41488

American (AMR) AF: 0.252 AC: 3840 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.188 AC: 652 AN: 3470

East Asian (EAS) AF: 0.150 AC: 778 AN: 5172

South Asian (SAS) AF: 0.345 AC: 1662 AN: 4820

European-Finnish (FIN) AF: 0.224 AC: 2370 AN: 10594

Middle Eastern (MID) AF: 0.284 AC: 83 AN: 292

European-Non Finnish (NFE) AF: 0.276 AC: 18747 AN: 67922

Other (OTH) AF: 0.338 AC: 713 AN: 2108

Alfa AF: 0.298 Hom.: 14746

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
PhyloP100		-0.040

Splicing

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

Other links and lift over

dbSNP: rs1972373; hg19: chr14-20445370;