chr1-22670078-T-C

Variant names:

• chr1-22670078-T-C
• rs7549747

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 0.5 in 152,080 control chromosomes in the GnomAD database, including 20,532 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 0.50 (20532 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.80
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.721 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: 0.499 AC: 75874 AN: 151960 Hom.: 20489 Cov.: 33

Gnomad AFR AF: 0.728

Gnomad AMI AF: 0.383

Gnomad AMR AF: 0.452

Gnomad ASJ AF: 0.401

Gnomad EAS AF: 0.422

Gnomad SAS AF: 0.499

Gnomad FIN AF: 0.351

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.407

Gnomad OTH AF: 0.491

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

GnomAD4 genome AF: 0.500 AC: 75974 AN: 152080 Hom.: 20532 Cov.: 33 AF XY: 0.495 AC XY: 36812 AN XY: 74346

African (AFR) AF: 0.728 AC: 30211 AN: 41482

American (AMR) AF: 0.452 AC: 6905 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.401 AC: 1393 AN: 3470

East Asian (EAS) AF: 0.423 AC: 2184 AN: 5168

South Asian (SAS) AF: 0.499 AC: 2400 AN: 4814

European-Finnish (FIN) AF: 0.351 AC: 3715 AN: 10574

Middle Eastern (MID) AF: 0.367 AC: 108 AN: 294

European-Non Finnish (NFE) AF: 0.407 AC: 27667 AN: 67972

Other (OTH) AF: 0.492 AC: 1042 AN: 2116

Alfa AF: 0.430 Hom.: 28980

Bravo AF: 0.517

Asia WGS AF: 0.511 AC: 1778 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.0020
DANN	Benign	0.38
PhyloP100		-2.8

Splicing

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

Other links and lift over

dbSNP: rs7549747; hg19: chr1-22996571;