chr7-5581212-C-G

Variant names:

• chr7-5581212-C-G
• rs1106076

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 0.374 in 151,852 control chromosomes in the GnomAD database, including 11,930 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 0.37 (11930 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.267
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.568 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: 0.374 AC: 56714 AN: 151734 Hom.: 11893 Cov.: 31

Gnomad AFR AF: 0.573

Gnomad AMI AF: 0.195

Gnomad AMR AF: 0.340

Gnomad ASJ AF: 0.310

Gnomad EAS AF: 0.203

Gnomad SAS AF: 0.407

Gnomad FIN AF: 0.300

Gnomad MID AF: 0.341

Gnomad NFE AF: 0.288

Gnomad OTH AF: 0.368

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

GnomAD4 genome AF: 0.374 AC: 56820 AN: 151852 Hom.: 11930 Cov.: 31 AF XY: 0.373 AC XY: 27691 AN XY: 74202

African (AFR) AF: 0.574 AC: 23741 AN: 41376

American (AMR) AF: 0.340 AC: 5178 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.310 AC: 1078 AN: 3472

East Asian (EAS) AF: 0.204 AC: 1051 AN: 5160

South Asian (SAS) AF: 0.408 AC: 1963 AN: 4812

European-Finnish (FIN) AF: 0.300 AC: 3166 AN: 10562

Middle Eastern (MID) AF: 0.353 AC: 103 AN: 292

European-Non Finnish (NFE) AF: 0.288 AC: 19584 AN: 67948

Other (OTH) AF: 0.370 AC: 779 AN: 2104

Alfa AF: 0.216 Hom.: 560

Bravo AF: 0.380

Asia WGS AF: 0.396 AC: 1375 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.93
DANN	Benign	0.41
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs1106076; hg19: chr7-5620843;