chr1-97009739-C-T

Position:

• chr1-97009739-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0228 in 152,276 control chromosomes in the GnomAD database, including 47 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 0.023 (47 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0850

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0228 (3478/152276) while in subpopulation NFE AF= 0.0325 (2214/68022). AF 95% confidence interval is 0.0314. There are 47 homozygotes in gnomad4. There are 1631 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 47 gene

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: 0.0229 AC: 3481 AN: 152158 Hom.: 47 Cov.: 33

Gnomad AFR AF: 0.00982

Gnomad AMI AF: 0.0285

Gnomad AMR AF: 0.0216

Gnomad ASJ AF: 0.0167

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0265

Gnomad FIN AF: 0.0229

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0325

Gnomad OTH AF: 0.0292

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

GnomAD4 genome AF: 0.0228 AC: 3478 AN: 152276 Hom.: 47 Cov.: 33 AF XY: 0.0219 AC XY: 1631 AN XY: 74456

Gnomad4 AFR AF: 0.00977

Gnomad4 AMR AF: 0.0216

Gnomad4 ASJ AF: 0.0167

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0267

Gnomad4 FIN AF: 0.0229

Gnomad4 NFE AF: 0.0325

Gnomad4 OTH AF: 0.0289

Alfa AF: 0.00774 Hom.: 0

Bravo AF: 0.0222

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.7
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12123160; hg19: chr1-97475295;