7-121322110-A-G

Variant names:

• chr7-121322110-A-G
• rs2908007

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 0.539 in 152,094 control chromosomes in the GnomAD database, including 25,454 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 0.54 (25454 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0960
• Publications: 36 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.856 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: 0.539 AC: 81852 AN: 151976 Hom.: 25408 Cov.: 33

Gnomad AFR AF: 0.863

Gnomad AMI AF: 0.324

Gnomad AMR AF: 0.441

Gnomad ASJ AF: 0.499

Gnomad EAS AF: 0.528

Gnomad SAS AF: 0.593

Gnomad FIN AF: 0.332

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.398

Gnomad OTH AF: 0.518

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

GnomAD4 genome AF: 0.539 AC: 81953 AN: 152094 Hom.: 25454 Cov.: 33 AF XY: 0.533 AC XY: 39601 AN XY: 74350

African (AFR) AF: 0.863 AC: 35833 AN: 41514

American (AMR) AF: 0.440 AC: 6728 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.499 AC: 1730 AN: 3468

East Asian (EAS) AF: 0.527 AC: 2725 AN: 5170

South Asian (SAS) AF: 0.591 AC: 2849 AN: 4818

European-Finnish (FIN) AF: 0.332 AC: 3510 AN: 10584

Middle Eastern (MID) AF: 0.517 AC: 152 AN: 294

European-Non Finnish (NFE) AF: 0.398 AC: 27027 AN: 67956

Other (OTH) AF: 0.525 AC: 1106 AN: 2106

Alfa AF: 0.446 Hom.: 65944

Bravo AF: 0.560

Asia WGS AF: 0.587 AC: 2041 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	7.5
DANN	Benign	0.54
PhyloP100		0.096

Splicing

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

Other links and lift over

dbSNP: rs2908007; hg19: chr7-120962164;