1-101118107-T-G

Variant names:

• chr1-101118107-T-G
• rs7528842

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 0.26 in 152,066 control chromosomes in the GnomAD database, including 5,642 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 0.26 (5642 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00900
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.368 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.260 AC: 39432 AN: 151948 Hom.: 5619 Cov.: 32

Gnomad AFR AF: 0.372

Gnomad AMI AF: 0.159

Gnomad AMR AF: 0.220

Gnomad ASJ AF: 0.295

Gnomad EAS AF: 0.120

Gnomad SAS AF: 0.122

Gnomad FIN AF: 0.127

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.240

Gnomad OTH AF: 0.278

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

GnomAD4 genome AF: 0.260 AC: 39503 AN: 152066 Hom.: 5642 Cov.: 32 AF XY: 0.251 AC XY: 18650 AN XY: 74346

African (AFR) AF: 0.373 AC: 15455 AN: 41462

American (AMR) AF: 0.219 AC: 3339 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.295 AC: 1023 AN: 3468

East Asian (EAS) AF: 0.120 AC: 621 AN: 5178

South Asian (SAS) AF: 0.121 AC: 585 AN: 4822

European-Finnish (FIN) AF: 0.127 AC: 1352 AN: 10608

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.240 AC: 16304 AN: 67968

Other (OTH) AF: 0.283 AC: 597 AN: 2112

Alfa AF: 0.243 Hom.: 5300

Bravo AF: 0.273

Asia WGS AF: 0.178 AC: 619 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.7
DANN	Benign	0.38
PhyloP100		0.0090

Splicing

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

Other links and lift over

dbSNP: rs7528842; hg19: chr1-101583663;