1-85587205-C-T

Position:

• chr1-85587205-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 0.0449 in 152,288 control chromosomes in the GnomAD database, including 153 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 0.045 (153 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.559

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0449 (6838/152288) while in subpopulation NFE AF= 0.0511 (3475/68008). AF 95% confidence interval is 0.0497. There are 153 homozygotes in gnomad4. There are 3277 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 153 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: 0.0448 AC: 6824 AN: 152170 Hom.: 154 Cov.: 33

Gnomad AFR AF: 0.0396

Gnomad AMI AF: 0.0746

Gnomad AMR AF: 0.0443

Gnomad ASJ AF: 0.0622

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.0263

Gnomad FIN AF: 0.0445

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0511

Gnomad OTH AF: 0.0574

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

GnomAD4 genome AF: 0.0449 AC: 6838 AN: 152288 Hom.: 153 Cov.: 33 AF XY: 0.0440 AC XY: 3277 AN XY: 74472

Gnomad4 AFR AF: 0.0398

Gnomad4 AMR AF: 0.0444

Gnomad4 ASJ AF: 0.0622

Gnomad4 EAS AF: 0.000579

Gnomad4 SAS AF: 0.0269

Gnomad4 FIN AF: 0.0445

Gnomad4 NFE AF: 0.0511

Gnomad4 OTH AF: 0.0568

Alfa AF: 0.0362 Hom.: 27

Bravo AF: 0.0441

Asia WGS AF: 0.0130 AC: 45 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	11
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12756618; hg19: chr1-86052888;