1-105431244-T-A

Position:

• chr1-105431244-T-A

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 0.0231 in 152,036 control chromosomes in the GnomAD database, including 62 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 (62 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0850

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BS1: Variant frequency is greater than expected in population amr. gnomad4 allele frequency = 0.0231 (3518/152036) while in subpopulation AMR AF= 0.0375 (572/15256). AF 95% confidence interval is 0.035. There are 62 homozygotes in gnomad4. There are 1707 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 62 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.105431244T>A		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0232 AC: 3522 AN: 151920 Hom.: 63 Cov.: 33

Gnomad AFR AF: 0.0292

Gnomad AMI AF: 0.0274

Gnomad AMR AF: 0.0377

Gnomad ASJ AF: 0.0433

Gnomad EAS AF: 0.000386

Gnomad SAS AF: 0.0180

Gnomad FIN AF: 0.00245

Gnomad MID AF: 0.131

Gnomad NFE AF: 0.0197

Gnomad OTH AF: 0.0340

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

GnomAD4 genome AF: 0.0231 AC: 3518 AN: 152036 Hom.: 62 Cov.: 33 AF XY: 0.0230 AC XY: 1707 AN XY: 74336

Gnomad4 AFR AF: 0.0291

Gnomad4 AMR AF: 0.0375

Gnomad4 ASJ AF: 0.0433

Gnomad4 EAS AF: 0.000387

Gnomad4 SAS AF: 0.0184

Gnomad4 FIN AF: 0.00245

Gnomad4 NFE AF: 0.0197

Gnomad4 OTH AF: 0.0332

Alfa AF: 0.0207 Hom.: 8

Bravo AF: 0.0269

Asia WGS AF: 0.0100 AC: 35 AN: 3448

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.87
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10494029; hg19: chr1-105973866;