7-106194837-A-G

Variant names:

• chr7-106194837-A-G
• rs887882

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 0.401 in 152,110 control chromosomes in the GnomAD database, including 12,681 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 0.40 (12681 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.864
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.524 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: 0.401 AC: 61024 AN: 151994 Hom.: 12689 Cov.: 32

Gnomad AFR AF: 0.304

Gnomad AMI AF: 0.362

Gnomad AMR AF: 0.383

Gnomad ASJ AF: 0.429

Gnomad EAS AF: 0.541

Gnomad SAS AF: 0.511

Gnomad FIN AF: 0.495

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.431

Gnomad OTH AF: 0.389

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

GnomAD4 genome AF: 0.401 AC: 61036 AN: 152110 Hom.: 12681 Cov.: 32 AF XY: 0.408 AC XY: 30303 AN XY: 74332

African (AFR) AF: 0.304 AC: 12616 AN: 41522

American (AMR) AF: 0.383 AC: 5858 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.429 AC: 1487 AN: 3468

East Asian (EAS) AF: 0.540 AC: 2791 AN: 5166

South Asian (SAS) AF: 0.511 AC: 2463 AN: 4824

European-Finnish (FIN) AF: 0.495 AC: 5231 AN: 10576

Middle Eastern (MID) AF: 0.425 AC: 125 AN: 294

European-Non Finnish (NFE) AF: 0.431 AC: 29313 AN: 67954

Other (OTH) AF: 0.390 AC: 823 AN: 2110

Alfa AF: 0.408 Hom.: 2029

Bravo AF: 0.387

Asia WGS AF: 0.485 AC: 1686 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.0050
DANN	Benign	0.47
PhyloP100		-0.86

Splicing

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

Other links and lift over

dbSNP: rs887882; hg19: chr7-105835283;