rs5745938

Positions:

• chr1-12165317-G-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 0.0273 in 152,220 control chromosomes in the GnomAD database, including 78 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 0.027 (78 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.499

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0273 (4154/152220) while in subpopulation NFE AF= 0.044 (2994/67980). AF 95% confidence interval is 0.0427. There are 78 homozygotes in gnomad4. There are 1883 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 78 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0273 AC: 4158 AN: 152102 Hom.: 78 Cov.: 32

Gnomad AFR AF: 0.00854

Gnomad AMI AF: 0.0461

Gnomad AMR AF: 0.0158

Gnomad ASJ AF: 0.0297

Gnomad EAS AF: 0.0137

Gnomad SAS AF: 0.0245

Gnomad FIN AF: 0.0166

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0441

Gnomad OTH AF: 0.0268

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

GnomAD4 genome AF: 0.0273 AC: 4154 AN: 152220 Hom.: 78 Cov.: 32 AF XY: 0.0253 AC XY: 1883 AN XY: 74424

Gnomad4 AFR AF: 0.00852

Gnomad4 AMR AF: 0.0158

Gnomad4 ASJ AF: 0.0297

Gnomad4 EAS AF: 0.0137

Gnomad4 SAS AF: 0.0243

Gnomad4 FIN AF: 0.0166

Gnomad4 NFE AF: 0.0440

Gnomad4 OTH AF: 0.0260

Alfa AF: 0.0304 Hom.: 11

Bravo AF: 0.0257

Asia WGS AF: 0.0200 AC: 70 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	0.16
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5745938; hg19: chr1-12225374; COSMIC: COSV66163765;