1-19983072-A-T

Variant names:

• chr1-19983072-A-T
• rs10916685

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 0.333 in 152,034 control chromosomes in the GnomAD database, including 8,678 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 0.33 (8678 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.303

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.368 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: 0.333 AC: 50633 AN: 151916 Hom.: 8675 Cov.: 32

Gnomad AFR AF: 0.290

Gnomad AMI AF: 0.442

Gnomad AMR AF: 0.376

Gnomad ASJ AF: 0.305

Gnomad EAS AF: 0.274

Gnomad SAS AF: 0.320

Gnomad FIN AF: 0.333

Gnomad MID AF: 0.252

Gnomad NFE AF: 0.356

Gnomad OTH AF: 0.320

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

GnomAD4 genome AF: 0.333 AC: 50656 AN: 152034 Hom.: 8678 Cov.: 32 AF XY: 0.333 AC XY: 24760 AN XY: 74312

Gnomad4 AFR AF: 0.290

Gnomad4 AMR AF: 0.376

Gnomad4 ASJ AF: 0.305

Gnomad4 EAS AF: 0.275

Gnomad4 SAS AF: 0.320

Gnomad4 FIN AF: 0.333

Gnomad4 NFE AF: 0.356

Gnomad4 OTH AF: 0.317

Alfa AF: 0.335 Hom.: 1089

Bravo AF: 0.338

Asia WGS AF: 0.319 AC: 1109 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	9.1
DANN	Benign	0.92

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10916685; hg19: chr1-20309565; COSMIC: COSV64287665;