1-220938438-T-G

Variant names:

• chr1-220938438-T-G
• rs7542375

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 0.388 in 151,226 control chromosomes in the GnomAD database, including 11,671 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 0.39 (11671 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.322
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.483 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: 0.388 AC: 58647 AN: 151108 Hom.: 11638 Cov.: 30

Gnomad AFR AF: 0.488

Gnomad AMI AF: 0.403

Gnomad AMR AF: 0.387

Gnomad ASJ AF: 0.325

Gnomad EAS AF: 0.400

Gnomad SAS AF: 0.421

Gnomad FIN AF: 0.333

Gnomad MID AF: 0.357

Gnomad NFE AF: 0.337

Gnomad OTH AF: 0.372

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

GnomAD4 genome AF: 0.388 AC: 58737 AN: 151226 Hom.: 11671 Cov.: 30 AF XY: 0.390 AC XY: 28794 AN XY: 73814

African (AFR) AF: 0.489 AC: 20113 AN: 41166

American (AMR) AF: 0.388 AC: 5858 AN: 15116

Ashkenazi Jewish (ASJ) AF: 0.325 AC: 1123 AN: 3456

East Asian (EAS) AF: 0.401 AC: 2058 AN: 5128

South Asian (SAS) AF: 0.420 AC: 2008 AN: 4776

European-Finnish (FIN) AF: 0.333 AC: 3481 AN: 10450

Middle Eastern (MID) AF: 0.373 AC: 109 AN: 292

European-Non Finnish (NFE) AF: 0.337 AC: 22834 AN: 67830

Other (OTH) AF: 0.374 AC: 788 AN: 2106

Alfa AF: 0.351 Hom.: 40278

Bravo AF: 0.396

Asia WGS AF: 0.430 AC: 1491 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.56
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs7542375; hg19: chr1-221111780;