chr1-86546420-C-A

Variant names:

• chr1-86546420-C-A
• rs11807638

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.138 in 152,058 control chromosomes in the GnomAD database, including 1,804 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 0.14 (1804 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.90
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.237 is higher than 0.05.

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: 0.138 AC: 20973 AN: 151940 Hom.: 1799 Cov.: 32

Gnomad AFR AF: 0.241

Gnomad AMI AF: 0.0680

Gnomad AMR AF: 0.103

Gnomad ASJ AF: 0.120

Gnomad EAS AF: 0.000386

Gnomad SAS AF: 0.0887

Gnomad FIN AF: 0.0614

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.111

Gnomad OTH AF: 0.131

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

GnomAD4 genome AF: 0.138 AC: 20999 AN: 152058 Hom.: 1804 Cov.: 32 AF XY: 0.134 AC XY: 9933 AN XY: 74350

African (AFR) AF: 0.241 AC: 9985 AN: 41440

American (AMR) AF: 0.102 AC: 1563 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.120 AC: 416 AN: 3470

East Asian (EAS) AF: 0.000387 AC: 2 AN: 5174

South Asian (SAS) AF: 0.0882 AC: 425 AN: 4820

European-Finnish (FIN) AF: 0.0614 AC: 649 AN: 10568

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.111 AC: 7572 AN: 67994

Other (OTH) AF: 0.130 AC: 273 AN: 2108

Alfa AF: 0.0246 Hom.: 21

Bravo AF: 0.144

Asia WGS AF: 0.0490 AC: 171 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.25
DANN	Benign	0.30
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs11807638; hg19: chr1-87012103;