rs7100400

Variant names:

• chr10-6082117-A-G
• rs7100400

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 0.0349 in 152,176 control chromosomes in the GnomAD database, including 164 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 0.035 (164 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.387
• Publications: 5 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 = 0.132 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: 0.0349 AC: 5314 AN: 152058 Hom.: 163 Cov.: 31

Gnomad AFR AF: 0.00884

Gnomad AMI AF: 0.167

Gnomad AMR AF: 0.0313

Gnomad ASJ AF: 0.0179

Gnomad EAS AF: 0.140

Gnomad SAS AF: 0.0375

Gnomad FIN AF: 0.0303

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0435

Gnomad OTH AF: 0.0306

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

GnomAD4 genome AF: 0.0349 AC: 5317 AN: 152176 Hom.: 164 Cov.: 31 AF XY: 0.0348 AC XY: 2588 AN XY: 74418

African (AFR) AF: 0.00881 AC: 366 AN: 41528

American (AMR) AF: 0.0313 AC: 478 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0179 AC: 62 AN: 3466

East Asian (EAS) AF: 0.141 AC: 727 AN: 5172

South Asian (SAS) AF: 0.0374 AC: 180 AN: 4818

European-Finnish (FIN) AF: 0.0303 AC: 321 AN: 10594

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.0435 AC: 2957 AN: 67998

Other (OTH) AF: 0.0331 AC: 70 AN: 2112

Alfa AF: 0.0388 Hom.: 106

Bravo AF: 0.0343

Asia WGS AF: 0.102 AC: 353 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	1.8
DANN	Benign	0.80
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs7100400; hg19: chr10-6124080;