chr7-140221721-G-A

Variant names:

• chr7-140221721-G-A
• rs880290

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 0.238 in 151,924 control chromosomes in the GnomAD database, including 4,547 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 0.24 (4547 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.371
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.268 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: 0.238 AC: 36097 AN: 151806 Hom.: 4546 Cov.: 30

Gnomad AFR AF: 0.218

Gnomad AMI AF: 0.269

Gnomad AMR AF: 0.209

Gnomad ASJ AF: 0.375

Gnomad EAS AF: 0.0214

Gnomad SAS AF: 0.235

Gnomad FIN AF: 0.195

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.271

Gnomad OTH AF: 0.272

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

GnomAD4 genome AF: 0.238 AC: 36105 AN: 151924 Hom.: 4547 Cov.: 30 AF XY: 0.233 AC XY: 17318 AN XY: 74240

African (AFR) AF: 0.218 AC: 9028 AN: 41414

American (AMR) AF: 0.208 AC: 3175 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.375 AC: 1303 AN: 3472

East Asian (EAS) AF: 0.0216 AC: 112 AN: 5178

South Asian (SAS) AF: 0.235 AC: 1129 AN: 4808

European-Finnish (FIN) AF: 0.195 AC: 2060 AN: 10558

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.271 AC: 18404 AN: 67942

Other (OTH) AF: 0.269 AC: 567 AN: 2110

Alfa AF: 0.250 Hom.: 623

Bravo AF: 0.234

Asia WGS AF: 0.135 AC: 471 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.1
DANN	Benign	0.77
PhyloP100		0.37

Splicing

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

Other links and lift over

dbSNP: rs880290; hg19: chr7-139921521;