chr1-163558957-G-A

Variant names:

• chr1-163558957-G-A
• rs6679806

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 0.436 in 151,850 control chromosomes in the GnomAD database, including 14,529 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 0.44 (14529 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.124
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.524 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: 0.436 AC: 66167 AN: 151734 Hom.: 14507 Cov.: 31

Gnomad AFR AF: 0.394

Gnomad AMI AF: 0.238

Gnomad AMR AF: 0.445

Gnomad ASJ AF: 0.402

Gnomad EAS AF: 0.526

Gnomad SAS AF: 0.542

Gnomad FIN AF: 0.480

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.443

Gnomad OTH AF: 0.434

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

GnomAD4 genome AF: 0.436 AC: 66229 AN: 151850 Hom.: 14529 Cov.: 31 AF XY: 0.442 AC XY: 32812 AN XY: 74214

African (AFR) AF: 0.394 AC: 16307 AN: 41398

American (AMR) AF: 0.445 AC: 6786 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.402 AC: 1395 AN: 3466

East Asian (EAS) AF: 0.526 AC: 2693 AN: 5122

South Asian (SAS) AF: 0.542 AC: 2604 AN: 4808

European-Finnish (FIN) AF: 0.480 AC: 5064 AN: 10546

Middle Eastern (MID) AF: 0.432 AC: 127 AN: 294

European-Non Finnish (NFE) AF: 0.443 AC: 30114 AN: 67960

Other (OTH) AF: 0.438 AC: 922 AN: 2104

Alfa AF: 0.445 Hom.: 8039

Bravo AF: 0.432

Asia WGS AF: 0.517 AC: 1797 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.6
DANN	Benign	0.75
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs6679806; hg19: chr1-163528747;