1-85587205-C-T

Variant names:

• chr1-85587205-C-T
• rs12756618

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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 the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 153 gene

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: 0.0448 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

African (AFR) AF: 0.0398 AC: 1655 AN: 41566

American (AMR) AF: 0.0444 AC: 679 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0622 AC: 216 AN: 3470

East Asian (EAS) AF: 0.000579 AC: 3 AN: 5182

South Asian (SAS) AF: 0.0269 AC: 130 AN: 4826

European-Finnish (FIN) AF: 0.0445 AC: 472 AN: 10618

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.0511 AC: 3475 AN: 68008

Other (OTH) AF: 0.0568 AC: 120 AN: 2112

Alfa AF: 0.0468 Hom.: 303

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
PhyloP100		0.56

Splicing

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

Other links and lift over

dbSNP: rs12756618; hg19: chr1-86052888;