chr7-45227690-A-T

Variant names:

• chr7-45227690-A-T
• rs6463270

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 0.233 in 151,974 control chromosomes in the GnomAD database, including 4,440 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 0.23 (4440 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.976
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.334 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: 0.233 AC: 35319 AN: 151856 Hom.: 4430 Cov.: 32

Gnomad AFR AF: 0.339

Gnomad AMI AF: 0.190

Gnomad AMR AF: 0.243

Gnomad ASJ AF: 0.255

Gnomad EAS AF: 0.186

Gnomad SAS AF: 0.169

Gnomad FIN AF: 0.184

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.180

Gnomad OTH AF: 0.231

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

GnomAD4 genome AF: 0.233 AC: 35352 AN: 151974 Hom.: 4440 Cov.: 32 AF XY: 0.234 AC XY: 17363 AN XY: 74278

African (AFR) AF: 0.339 AC: 14026 AN: 41404

American (AMR) AF: 0.243 AC: 3713 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.255 AC: 887 AN: 3472

East Asian (EAS) AF: 0.185 AC: 958 AN: 5166

South Asian (SAS) AF: 0.168 AC: 808 AN: 4820

European-Finnish (FIN) AF: 0.184 AC: 1947 AN: 10562

Middle Eastern (MID) AF: 0.303 AC: 89 AN: 294

European-Non Finnish (NFE) AF: 0.180 AC: 12259 AN: 67966

Other (OTH) AF: 0.233 AC: 492 AN: 2114

Alfa AF: 0.0821 Hom.: 107

Bravo AF: 0.241

Asia WGS AF: 0.209 AC: 727 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.7
DANN	Benign	0.78
PhyloP100		0.98

Splicing

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

Other links and lift over

dbSNP: rs6463270; hg19: chr7-45267289;